diff --git a/pipestat/parsed_schema.py b/pipestat/parsed_schema.py
index ed4ea6c8..f8830efc 100644
--- a/pipestat/parsed_schema.py
+++ b/pipestat/parsed_schema.py
@@ -95,10 +95,16 @@ def __init__(self, data: Union[Dict[str, Any], Path, str]) -> None:
 
             self._pipeline_name = data["properties"].pop(SCHEMA_PIPELINE_NAME_KEY, None)
 
+            # Two passes for sample-data as it is now nested under items per #204
             sample_data = _safe_pop_one_mapping(
                 subkeys=["samples"],
                 data=data["properties"],
                 info_name="sample-level",
+                mappingkey="items",
+            )
+            sample_data = _safe_pop_one_mapping(
+                data=sample_data,
+                info_name="sample-level",
                 mappingkey="properties",
             )
 
diff --git a/tests/data/output_schema.yaml b/tests/data/output_schema.yaml
index d4ecbc1e..01f83fff 100644
--- a/tests/data/output_schema.yaml
+++ b/tests/data/output_schema.yaml
@@ -4,9 +4,11 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-        result_name:
-          type: string
-          description: "ResultName"
+    type: array
+    items:
+      type: object
+      properties:
+          result_name:
+            type: string
+            description: "ResultName"
 
diff --git a/tests/data/output_schema_as_JSON_schema.yaml b/tests/data/output_schema_as_JSON_schema.yaml
index 64582f20..d8cc84f4 100644
--- a/tests/data/output_schema_as_JSON_schema.yaml
+++ b/tests/data/output_schema_as_JSON_schema.yaml
@@ -4,54 +4,56 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-        number_of_things:
-          type: integer
-          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit."
-        output_image:
-          $ref: "#/$defs/image"
-          description: "This an output image"
-        output_file:
-          $ref: "#/$defs/file"
-          description: "This a path to the output image"
-        collection_of_images:
-          type: array
-          description: A collection of images.
-          items:
+    type: array
+    items:
+      type: object
+      properties:
+          number_of_things:
+            type: integer
+            description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit."
+          output_image:
+            $ref: "#/$defs/image"
+            description: "This an output image"
+          output_file:
+            $ref: "#/$defs/file"
+            description: "This a path to the output image"
+          collection_of_images:
+            type: array
+            description: A collection of images.
+            items:
+              type: object
+              properties:
+                prop1:
+                  $ref: "#/$defs/file"
+                  description: An example file.
+          nested_object:
             type: object
+            description: An object containing output file and image.
             properties:
-              prop1:
+              example_property_1:
                 $ref: "#/$defs/file"
                 description: An example file.
-        nested_object:
-          type: object
-          description: An object containing output file and image.
-          properties:
-            example_property_1:
-              $ref: "#/$defs/file"
-              description: An example file.
-            example_property_2:
-              $ref: "#/$defs/image"
-              description: An example image.
-        output_file_nested_object:
-          type: object
-          description: First Level
-          properties:
-            example_property_1:
-              type: object
-              description: Second Level
-              properties:
-                third_level_property_1:
-                  $ref: "#/$defs/file"
-                  description: Third Level
-            example_property_2:
-              type: object
-              description: Second Level
-              properties:
-                third_level_property_1:
-                  $ref: "#/$defs/file"
-                  description: Third Level
+              example_property_2:
+                $ref: "#/$defs/image"
+                description: An example image.
+          output_file_nested_object:
+            type: object
+            description: First Level
+            properties:
+              example_property_1:
+                type: object
+                description: Second Level
+                properties:
+                  third_level_property_1:
+                    $ref: "#/$defs/file"
+                    description: Third Level
+              example_property_2:
+                type: object
+                description: Second Level
+                properties:
+                  third_level_property_1:
+                    $ref: "#/$defs/file"
+                    description: Third Level
 $defs:
   image:
     type: object
diff --git a/tests/data/output_schema_html_report.yaml b/tests/data/output_schema_html_report.yaml
index 46a88e7d..f1dd0eda 100644
--- a/tests/data/output_schema_html_report.yaml
+++ b/tests/data/output_schema_html_report.yaml
@@ -19,26 +19,28 @@ properties:
         type: boolean
         description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras pharetra."
   samples:
-    type: object
-    properties:
-      smooth_bw:
-        path: "aligned_{genome}/{sample_name}_smooth.bw"
-        type: string
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
-      aligned_bam:
-        path: "aligned_{genome}/{sample_name}_sort.bam"
-        type: string
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus ipsum erat, porta in condimentum viverra, pellentesque in nisl. Nulla rhoncus nibh est, quis malesuada diam suscipit at. In ut diam."
-      peaks_bed:
-        path: "peak_calling_{genome}/{sample_name}_peaks.bed"
-        type: string
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
-      output_file:
-        $ref: "#/$defs/file"
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
-      output_image:
-        $ref: "#/$defs/image"
-        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras pharetra."
+    type: array
+    items:
+      type: object
+      properties:
+        smooth_bw:
+          path: "aligned_{genome}/{sample_name}_smooth.bw"
+          type: string
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
+        aligned_bam:
+          path: "aligned_{genome}/{sample_name}_sort.bam"
+          type: string
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus ipsum erat, porta in condimentum viverra, pellentesque in nisl. Nulla rhoncus nibh est, quis malesuada diam suscipit at. In ut diam."
+        peaks_bed:
+          path: "peak_calling_{genome}/{sample_name}_peaks.bed"
+          type: string
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
+        output_file:
+          $ref: "#/$defs/file"
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
+        output_image:
+          $ref: "#/$defs/image"
+          description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras pharetra."
 $defs:
   image:
     type: object
diff --git a/tests/data/sample_output_schema.yaml b/tests/data/sample_output_schema.yaml
index 3211ccdd..eb7bbd2d 100644
--- a/tests/data/sample_output_schema.yaml
+++ b/tests/data/sample_output_schema.yaml
@@ -4,30 +4,32 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-      number_of_things:
-        type: integer
-        description: "Number of things"
-      percentage_of_things:
-        type: number
-        description: "Percentage of things"
-      name_of_something:
-        type: string
-        description: "Name of something"
-      switch_value:
-        type: boolean
-        description: "Is the switch on or off"
-      output_file:
-        $ref: "#/$defs/file"
-        description: "This a path to the output file"
-      output_image:
-        $ref: "#/$defs/image"
-        description: "This a path to the output image"
-      md5sum:
-        type: string
-        description: "MD5SUM of an object"
-        highlight: true
+    type: array
+    items:
+      type: object
+      properties:
+        number_of_things:
+          type: integer
+          description: "Number of things"
+        percentage_of_things:
+          type: number
+          description: "Percentage of things"
+        name_of_something:
+          type: string
+          description: "Name of something"
+        switch_value:
+          type: boolean
+          description: "Is the switch on or off"
+        output_file:
+          $ref: "#/$defs/file"
+          description: "This a path to the output file"
+        output_image:
+          $ref: "#/$defs/image"
+          description: "This a path to the output image"
+        md5sum:
+          type: string
+          description: "MD5SUM of an object"
+          highlight: true
 $defs:
   image:
     type: object
diff --git a/tests/data/sample_output_schema__with_project_with_samples_with_status.yaml b/tests/data/sample_output_schema__with_project_with_samples_with_status.yaml
index e5d48a1c..e70d63ec 100644
--- a/tests/data/sample_output_schema__with_project_with_samples_with_status.yaml
+++ b/tests/data/sample_output_schema__with_project_with_samples_with_status.yaml
@@ -19,20 +19,22 @@ properties:
         type: boolean
         description: "Is the switch on or off"
   samples:
-    type: object
-    properties:
-      smooth_bw:
-        path: "aligned_{genome}/{sample_name}_smooth.bw"
-        type: string
-        description: "A smooth bigwig file"
-      aligned_bam:
-        path: "aligned_{genome}/{sample_name}_sort.bam"
-        type: string
-        description: "A sorted, aligned BAM file"
-      peaks_bed:
-        path: "peak_calling_{genome}/{sample_name}_peaks.bed"
-        type: string
-        description: "Peaks in BED format"
+    type: array
+    items:
+      type: object
+      properties:
+        smooth_bw:
+          path: "aligned_{genome}/{sample_name}_smooth.bw"
+          type: string
+          description: "A smooth bigwig file"
+        aligned_bam:
+          path: "aligned_{genome}/{sample_name}_sort.bam"
+          type: string
+          description: "A sorted, aligned BAM file"
+        peaks_bed:
+          path: "peak_calling_{genome}/{sample_name}_peaks.bed"
+          type: string
+          description: "Peaks in BED format"
   status:
     type: object
     properties:
diff --git a/tests/data/sample_output_schema__with_project_with_samples_without_status.yaml b/tests/data/sample_output_schema__with_project_with_samples_without_status.yaml
index 649abdaa..4a44d4ce 100644
--- a/tests/data/sample_output_schema__with_project_with_samples_without_status.yaml
+++ b/tests/data/sample_output_schema__with_project_with_samples_without_status.yaml
@@ -19,17 +19,19 @@ properties:
         type: boolean
         description: "Is the switch on or off"
   samples:
-    type: object
-    properties:
-      smooth_bw:
-        path: "aligned_{genome}/{sample_name}_smooth.bw"
-        type: string
-        description: "A smooth bigwig file"
-      aligned_bam:
-        path: "aligned_{genome}/{sample_name}_sort.bam"
-        type: string
-        description: "A sorted, aligned BAM file"
-      peaks_bed:
-        path: "peak_calling_{genome}/{sample_name}_peaks.bed"
-        type: string
-        description: "Peaks in BED format"
+    type: array
+    items:
+      type: object
+      properties:
+        smooth_bw:
+          path: "aligned_{genome}/{sample_name}_smooth.bw"
+          type: string
+          description: "A smooth bigwig file"
+        aligned_bam:
+          path: "aligned_{genome}/{sample_name}_sort.bam"
+          type: string
+          description: "A sorted, aligned BAM file"
+        peaks_bed:
+          path: "peak_calling_{genome}/{sample_name}_peaks.bed"
+          type: string
+          description: "Peaks in BED format"
diff --git a/tests/data/sample_output_schema__without_project_with_samples_with_status.yaml b/tests/data/sample_output_schema__without_project_with_samples_with_status.yaml
index 577f7ec6..bf76a542 100644
--- a/tests/data/sample_output_schema__without_project_with_samples_with_status.yaml
+++ b/tests/data/sample_output_schema__without_project_with_samples_with_status.yaml
@@ -4,20 +4,22 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-      smooth_bw:
-        path: "aligned_{genome}/{sample_name}_smooth.bw"
-        type: string
-        description: "A smooth bigwig file"
-      aligned_bam:
-        path: "aligned_{genome}/{sample_name}_sort.bam"
-        type: string
-        description: "A sorted, aligned BAM file"
-      peaks_bed:
-        path: "peak_calling_{genome}/{sample_name}_peaks.bed"
-        type: string
-        description: "Peaks in BED format"
+    type: array
+    items:
+      type: object
+      properties:
+        smooth_bw:
+          path: "aligned_{genome}/{sample_name}_smooth.bw"
+          type: string
+          description: "A smooth bigwig file"
+        aligned_bam:
+          path: "aligned_{genome}/{sample_name}_sort.bam"
+          type: string
+          description: "A sorted, aligned BAM file"
+        peaks_bed:
+          path: "peak_calling_{genome}/{sample_name}_peaks.bed"
+          type: string
+          description: "Peaks in BED format"
   status:
     type: object
     properties:
diff --git a/tests/data/sample_output_schema__without_project_with_samples_without_status.yaml b/tests/data/sample_output_schema__without_project_with_samples_without_status.yaml
index 501f1bb1..f329ebcc 100644
--- a/tests/data/sample_output_schema__without_project_with_samples_without_status.yaml
+++ b/tests/data/sample_output_schema__without_project_with_samples_without_status.yaml
@@ -4,17 +4,19 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-      smooth_bw:
-        path: "aligned_{genome}/{sample_name}_smooth.bw"
-        type: string
-        description: "A smooth bigwig file"
-      aligned_bam:
-        path: "aligned_{genome}/{sample_name}_sort.bam"
-        type: string
-        description: "A sorted, aligned BAM file"
-      peaks_bed:
-        path: "peak_calling_{genome}/{sample_name}_peaks.bed"
-        type: string
-        description: "Peaks in BED format"
+    type: array
+    items:
+      type: object
+      properties:
+        smooth_bw:
+          path: "aligned_{genome}/{sample_name}_smooth.bw"
+          type: string
+          description: "A smooth bigwig file"
+        aligned_bam:
+          path: "aligned_{genome}/{sample_name}_sort.bam"
+          type: string
+          description: "A sorted, aligned BAM file"
+        peaks_bed:
+          path: "peak_calling_{genome}/{sample_name}_peaks.bed"
+          type: string
+          description: "Peaks in BED format"
diff --git a/tests/data/sample_output_schema_highlight.yaml b/tests/data/sample_output_schema_highlight.yaml
index 7d5dbc16..06acfa37 100644
--- a/tests/data/sample_output_schema_highlight.yaml
+++ b/tests/data/sample_output_schema_highlight.yaml
@@ -4,49 +4,51 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-      number_of_things:
-        type: integer
-        description: "Number of things"
-      percentage_of_things:
-        type: number
-        description: "Percentage of things"
-      name_of_something:
-        type: string
-        description: "Name of something"
-      switch_value:
-        type: boolean
-        description: "Is the switch on or off"
-      collection_of_things:
-        type: array
-        description: "This store collection of values"
-      output_object:
-        type: object
-        description: "Object output"
-      output_file:
-        $ref: "#/$defs/file"
-        description: "This a path to the output file"
-      output_image:
-        $ref: "#/$defs/image"
-        highlight: false
-        description: "This a path to the output image"
-      log:
-        $ref: "#/$defs/file"
-        highlight: true
-        description: "The log file of the pipeline run"
-      profile:
-        $ref: "#/$defs/file"
-        highlight: true
-        description: "The profile of the pipeline run"
-      commands:
-        $ref: "#/$defs/file"
-        highlight: true
-        description: "The file with shell commands executed by this pipeline"
-      version:
-        type: string
-        highlight: true
-        description: "Pipeline version"
+    type: array
+    items:
+      type: object
+      properties:
+        number_of_things:
+          type: integer
+          description: "Number of things"
+        percentage_of_things:
+          type: number
+          description: "Percentage of things"
+        name_of_something:
+          type: string
+          description: "Name of something"
+        switch_value:
+          type: boolean
+          description: "Is the switch on or off"
+        collection_of_things:
+          type: array
+          description: "This store collection of values"
+        output_object:
+          type: object
+          description: "Object output"
+        output_file:
+          $ref: "#/$defs/file"
+          description: "This a path to the output file"
+        output_image:
+          $ref: "#/$defs/image"
+          highlight: false
+          description: "This a path to the output image"
+        log:
+          $ref: "#/$defs/file"
+          highlight: true
+          description: "The log file of the pipeline run"
+        profile:
+          $ref: "#/$defs/file"
+          highlight: true
+          description: "The profile of the pipeline run"
+        commands:
+          $ref: "#/$defs/file"
+          highlight: true
+          description: "The file with shell commands executed by this pipeline"
+        version:
+          type: string
+          highlight: true
+          description: "Pipeline version"
 $defs:
   image:
     type: object
diff --git a/tests/data/sample_output_schema_recursive.yaml b/tests/data/sample_output_schema_recursive.yaml
index 1e315a88..ee916039 100644
--- a/tests/data/sample_output_schema_recursive.yaml
+++ b/tests/data/sample_output_schema_recursive.yaml
@@ -4,59 +4,61 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-      number_of_things:
-        type: integer
-        description: "Number of things"
-      percentage_of_things:
-        type: number
-        description: "Percentage of things"
-      name_of_something:
-        type: string
-        description: "Name of something"
-      switch_value:
-        type: boolean
-        description: "Is the switch on or off"
-      md5sum:
-        type: string
-        description: "MD5SUM of an object"
-        highlight: true
-      collection_of_images:
-        description: "This store collection of values or objects"
-        type: array
-        items:
-          properties:
-              prop1:
-                description: "This is an example file"
-                $ref: "#/$defs/file"
-      output_file_in_object:
-        type: object
-        properties:
-          prop1:
-            description: "This is an example file"
-            $ref: "#/$defs/file"
-          prop2:
-            description: "This is an example image"
-            $ref: "#/$defs/image"
-        description: "Object output"
-      output_file_in_object_nested:
-        type: object
-        description: First Level
-        properties:
-          prop1:
-            type: object
-            description: Second Level
+    type: array
+    items:
+      type: object
+      properties:
+        number_of_things:
+          type: integer
+          description: "Number of things"
+        percentage_of_things:
+          type: number
+          description: "Percentage of things"
+        name_of_something:
+          type: string
+          description: "Name of something"
+        switch_value:
+          type: boolean
+          description: "Is the switch on or off"
+        md5sum:
+          type: string
+          description: "MD5SUM of an object"
+          highlight: true
+        collection_of_images:
+          description: "This store collection of values or objects"
+          type: array
+          items:
             properties:
-              prop2:
-                type: integer
-                description: Third Level
-      output_file:
-        $ref: "#/$defs/file"
-        description: "This a path to the output file"
-      output_image:
-        $ref: "#/$defs/image"
-        description: "This a path to the output image"
+                prop1:
+                  description: "This is an example file"
+                  $ref: "#/$defs/file"
+        output_file_in_object:
+          type: object
+          properties:
+            prop1:
+              description: "This is an example file"
+              $ref: "#/$defs/file"
+            prop2:
+              description: "This is an example image"
+              $ref: "#/$defs/image"
+          description: "Object output"
+        output_file_in_object_nested:
+          type: object
+          description: First Level
+          properties:
+            prop1:
+              type: object
+              description: Second Level
+              properties:
+                prop2:
+                  type: integer
+                  description: Third Level
+        output_file:
+          $ref: "#/$defs/file"
+          description: "This a path to the output file"
+        output_image:
+          $ref: "#/$defs/image"
+          description: "This a path to the output image"
 $defs:
   image:
     type: object
diff --git a/tests/data/sample_output_schema_sqlite.yaml b/tests/data/sample_output_schema_sqlite.yaml
index d3687b72..5cd14543 100644
--- a/tests/data/sample_output_schema_sqlite.yaml
+++ b/tests/data/sample_output_schema_sqlite.yaml
@@ -4,11 +4,13 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-      number_of_things:
-        type: integer
-        description: "Number of things"
-      percentage_of_things:
-        type: number
-        description: "Percentage of things"
\ No newline at end of file
+    type: array
+    items:
+      type: object
+      properties:
+        number_of_things:
+          type: integer
+          description: "Number of things"
+        percentage_of_things:
+          type: number
+          description: "Percentage of things"
\ No newline at end of file
diff --git a/tests/data/sample_output_schema_with_index.yaml b/tests/data/sample_output_schema_with_index.yaml
index 6e48de7e..6b25a494 100644
--- a/tests/data/sample_output_schema_with_index.yaml
+++ b/tests/data/sample_output_schema_with_index.yaml
@@ -4,61 +4,63 @@ type: object
 properties:
   pipeline_name: "default_pipeline_name"
   samples:
-    type: object
-    properties:
-      number_of_things:
-        type: integer
-        description: "Number of things"
-      percentage_of_things:
-        type: number
-        description: "Percentage of things"
-      name_of_something:
-        type: string
-        description: "Name of something"
-      switch_value:
-        type: boolean
-        description: "Is the switch on or off"
-      md5sum:
-        type: string
-        description: "MD5SUM of an object"
-        highlight: true
-        index: True
-      collection_of_images:
-        description: "This store collection of values or objects"
-        type: array
-        items:
-          properties:
-              prop1:
-                description: "This is an example file"
-                $ref: "#/$defs/file"
-      output_file_in_object:
-        type: object
-        index: True
-        properties:
-          prop1:
-            description: "This is an example file"
-            $ref: "#/$defs/file"
-          prop2:
-            description: "This is an example image"
-            $ref: "#/$defs/image"
-        description: "Object output"
-      output_file_in_object_nested:
-        type: object
-        description: First Level
-        properties:
-          prop1:
-            type: object
-            description: Second Level
+    type: array
+    items:
+      type: object
+      properties:
+        number_of_things:
+          type: integer
+          description: "Number of things"
+        percentage_of_things:
+          type: number
+          description: "Percentage of things"
+        name_of_something:
+          type: string
+          description: "Name of something"
+        switch_value:
+          type: boolean
+          description: "Is the switch on or off"
+        md5sum:
+          type: string
+          description: "MD5SUM of an object"
+          highlight: true
+          index: True
+        collection_of_images:
+          description: "This store collection of values or objects"
+          type: array
+          items:
             properties:
-              prop2:
-                type: integer
-                description: Third Level
-      output_file:
-        $ref: "#/$defs/file"
-        description: "This a path to the output file"
-      output_image:
-        $ref: "#/$defs/image"
-        description: "This a path to the output image"
+                prop1:
+                  description: "This is an example file"
+                  $ref: "#/$defs/file"
+        output_file_in_object:
+          type: object
+          index: True
+          properties:
+            prop1:
+              description: "This is an example file"
+              $ref: "#/$defs/file"
+            prop2:
+              description: "This is an example image"
+              $ref: "#/$defs/image"
+          description: "Object output"
+        output_file_in_object_nested:
+          type: object
+          description: First Level
+          properties:
+            prop1:
+              type: object
+              description: Second Level
+              properties:
+                prop2:
+                  type: integer
+                  description: Third Level
+        output_file:
+          $ref: "#/$defs/file"
+          description: "This a path to the output file"
+        output_image:
+          $ref: "#/$defs/image"
+          description: "This a path to the output image"
 $defs:
   image:
     type: object