diff --git a/glotaran/analysis/problem_grouped.py b/glotaran/analysis/problem_grouped.py
index 7711f50ab..e898970b2 100644
--- a/glotaran/analysis/problem_grouped.py
+++ b/glotaran/analysis/problem_grouped.py
@@ -293,7 +293,12 @@ def calculate_residual(self):
         self._weighted_residuals = list(map(lambda result: result[2], results))
         self._residuals = list(map(lambda result: result[3], results))
         self._additional_penalty = calculate_clp_penalties(
-            self.model, self.parameters, self._clp_labels, self._grouped_clps, self._full_axis
+            self.model,
+            self.parameters,
+            self._clp_labels,
+            self._grouped_clps,
+            self._full_axis,
+            self.dataset_models,
         )
 
         return self._reduced_clps, self._clps, self._weighted_residuals, self._residuals
diff --git a/glotaran/analysis/problem_ungrouped.py b/glotaran/analysis/problem_ungrouped.py
index 10b03eff9..8b7fedb18 100644
--- a/glotaran/analysis/problem_ungrouped.py
+++ b/glotaran/analysis/problem_ungrouped.py
@@ -168,7 +168,12 @@ def _calculate_residual(self, label: str, dataset_model: DatasetModel):
 
         clp_labels = self._get_clp_labels(label)
         additional_penalty = calculate_clp_penalties(
-            self.model, self.parameters, clp_labels, self._clps[label], global_axis
+            self.model,
+            self.parameters,
+            clp_labels,
+            self._clps[label],
+            global_axis,
+            self.dataset_models,
         )
         if additional_penalty.size != 0:
             self._additional_penalty.append(additional_penalty)
diff --git a/glotaran/analysis/util.py b/glotaran/analysis/util.py
index d54cb06b0..e25e79136 100644
--- a/glotaran/analysis/util.py
+++ b/glotaran/analysis/util.py
@@ -194,27 +194,48 @@ def calculate_clp_penalties(
     clp_labels: list[list[str]] | list[str],
     clps: list[np.ndarray],
     global_axis: np.ndarray,
+    dataset_models: dict[str, DatasetModel],
 ) -> np.ndarray:
 
+    # TODO: make a decision on how to handle clp_penalties per dataset
+    # 1. sum up contributions per dataset on each dataset_axis (v0.4.1)
+    # 2. sum up contributions on the global_axis (future?)
+
     penalties = []
     for penalty in model.clp_area_penalties:
         penalty = penalty.fill(model, parameters)
-        source_area = _get_area(
-            penalty.source,
-            clp_labels,
-            clps,
-            penalty.source_intervals,
-            global_axis,
-        )
-
-        target_area = _get_area(
-            penalty.target,
-            clp_labels,
-            clps,
-            penalty.target_intervals,
-            global_axis,
-        )
-
+        source_area = np.array([])
+        target_area = np.array([])
+        for _, dataset_model in dataset_models.items():
+            dataset_axis = dataset_model.get_global_axis()
+
+            source_area = np.concatenate(
+                [
+                    source_area,
+                    _get_area(
+                        penalty.source,
+                        clp_labels,
+                        clps,
+                        penalty.source_intervals,
+                        global_axis,
+                        dataset_axis,
+                    ),
+                ]
+            )
+
+            target_area = np.concatenate(
+                [
+                    target_area,
+                    _get_area(
+                        penalty.target,
+                        clp_labels,
+                        clps,
+                        penalty.target_intervals,
+                        global_axis,
+                        dataset_axis,
+                    ),
+                ]
+            )
         area_penalty = np.abs(np.sum(source_area) - penalty.parameter * np.sum(target_area))
 
         penalties.append(area_penalty * penalty.weight)
@@ -228,14 +249,18 @@ def _get_area(
     clps: list[np.ndarray],
     intervals: list[tuple[float, float]],
     global_axis: np.ndarray,
+    dataset_axis: np.ndarray,
 ) -> np.ndarray:
     area = []
 
     for interval in intervals:
         if interval[0] > global_axis[-1]:
             continue
-
-        start_idx, end_idx = get_idx_from_interval(interval, global_axis)
+        bounded_interval = (
+            max(interval[0], np.min(dataset_axis)),
+            min(interval[1], np.max(dataset_axis)),
+        )
+        start_idx, end_idx = get_idx_from_interval(bounded_interval, global_axis)
         for i in range(start_idx, end_idx + 1):
             index_clp_labels = clp_labels[i] if isinstance(clp_labels[0], list) else clp_labels
             if clp_label in index_clp_labels:
diff --git a/glotaran/model/clp_penalties.py b/glotaran/model/clp_penalties.py
index 2918d9b41..3aa08ea32 100644
--- a/glotaran/model/clp_penalties.py
+++ b/glotaran/model/clp_penalties.py
@@ -73,6 +73,7 @@ def apply_spectral_penalties(
     group_tolerance: float,
 ) -> np.ndarray:
 
+    # TODO: seems to duplicate calculate_clp_penalties
     penalties = []
     for penalty in model.clp_area_penalties: