diff --git a/src/openforms/js/components/admin/form_design/variables/utils.js b/src/openforms/js/components/admin/form_design/variables/utils.js
index 393e75cf49..c4ec01238a 100644
--- a/src/openforms/js/components/admin/form_design/variables/utils.js
+++ b/src/openforms/js/components/admin/form_design/variables/utils.js
@@ -84,13 +84,26 @@ const shouldNotUpdateVariables = (newComponent, oldComponent, mutationType, step
   return isComponentWithVariable || isEditGridChild;
 };
 
+/**
+ * Transform the Formio configuration into FormVariable instances.
+ * @param  {String} formDefinition API resource of the form definition that the configuration belongs to.
+ * @param  {OBject} configuration  The Formio form configuration.
+ */
 const getFormVariables = (formDefinition, configuration) => {
   const newFormVariables = [];
 
   FormioUtils.eachComponent(configuration.components, component => {
     if (component.type === 'softRequiredErrors') return;
+
+    // sEE #5035 - the client side upload components variables are created on load, and
+    // then they get pushed to the server on save and are persisted too, which causes
+    // upload issues. This may even have been the root cause of this issue where
+    // "phantom" variables show up in the step data.
+    if (isInEditGrid(component, configuration)) return;
+
     newFormVariables.push(makeNewVariableFromComponent(component, formDefinition));
   });
+
   return newFormVariables;
 };
 
diff --git a/src/openforms/submissions/models/submission.py b/src/openforms/submissions/models/submission.py
index 8592e308c2..1fa6c42d4d 100644
--- a/src/openforms/submissions/models/submission.py
+++ b/src/openforms/submissions/models/submission.py
@@ -2,6 +2,7 @@
 
 import logging
 import uuid
+from copy import deepcopy
 from dataclasses import dataclass
 from typing import TYPE_CHECKING, Any, Mapping
 
@@ -429,9 +430,8 @@ def total_configuration_wrapper(self) -> FormioConfigurationWrapper:
             if len(form_steps) == 0:
                 return FormioConfigurationWrapper(configuration={})
 
-            wrapper = FormioConfigurationWrapper(
-                form_steps[0].form_definition.configuration
-            )
+            begin_configuration = deepcopy(form_steps[0].form_definition.configuration)
+            wrapper = FormioConfigurationWrapper(begin_configuration)
             for form_step in form_steps[1:]:
                 wrapper += form_step.form_definition.configuration_wrapper
             self._total_configuration_wrapper = wrapper
diff --git a/src/openforms/submissions/tests/test_models.py b/src/openforms/submissions/tests/test_models.py
index 282059960f..c6c5550844 100644
--- a/src/openforms/submissions/tests/test_models.py
+++ b/src/openforms/submissions/tests/test_models.py
@@ -456,3 +456,54 @@ def test_names_do_not_break_pdf_saving_to_disk(self):
         report.generate_submission_report_pdf()
 
         self.assertTrue(report.content.storage.exists(report.content.name))
+
+    @tag("gh-5035")
+    def test_total_configuration_wrapper_does_not_mutate_first_step(self):
+        form = FormFactory.create(
+            generate_minimal_setup=True,
+            formstep__form_definition__configuration={
+                "components": [
+                    {
+                        "key": "textfield1",
+                        "type": "textfield",
+                        "label": "textfield",
+                    }
+                ]
+            },
+        )
+        FormStepFactory.create(
+            form=form,
+            order=1,
+            form_definition__configuration={
+                "components": [
+                    {
+                        "key": "textfield2",
+                        "type": "textfield",
+                        "label": "Text field 2",
+                    }
+                ]
+            },
+        )
+        submission = SubmissionFactory.create(form=form)
+
+        configuration_wrapper = submission.total_configuration_wrapper
+
+        with self.subTest("all keys present"):
+            self.assertIn("textfield1", configuration_wrapper)
+            self.assertIn("textfield2", configuration_wrapper)
+
+        step1, step2 = submission.steps
+
+        with self.subTest("step 1 keys"):
+            step1_keys = [
+                c["key"]
+                for c in step1.form_step.form_definition.configuration["components"]
+            ]
+            self.assertEqual(step1_keys, ["textfield1"])
+
+        with self.subTest("step 2 keys"):
+            step2_keys = [
+                c["key"]
+                for c in step2.form_step.form_definition.configuration["components"]
+            ]
+            self.assertEqual(step2_keys, ["textfield2"])