diff --git a/cg/apps/demultiplex/sample_sheet/api.py b/cg/apps/demultiplex/sample_sheet/api.py
index be04e69815..9790ea0a4b 100644
--- a/cg/apps/demultiplex/sample_sheet/api.py
+++ b/cg/apps/demultiplex/sample_sheet/api.py
@@ -17,6 +17,7 @@
 from cg.io.controller import WriteFile, WriteStream
 from cg.meta.demultiplex.housekeeper_storage_functions import (
     add_and_include_sample_sheet_path_to_housekeeper,
+    delete_file_from_housekeeper,
 )
 from cg.models.flow_cell.flow_cell import FlowCellDirectoryData
 
@@ -76,13 +77,24 @@ def get_valid_sample_sheet_path(self, sample_sheet_path: Path) -> Path | None:
             LOG.warning(f"Sample sheet with path {sample_sheet_path} does not exist")
 
     def get_valid_sample_sheet_path_from_hk(self, flow_cell_id: str) -> Path | None:
-        """Return the sample sheet path from Housekeeper if is valid and exists."""
+        """
+        Return the sample sheet path from Housekeeper if is valid and exists. If it is invalid,
+        deletes it from Housekeeper database and bundle.
+        """
+        LOG.info("Getting sample sheet from Housekeeper")
         try:
             sample_sheet_path: Path | None = self.hk_api.get_sample_sheet_path(flow_cell_id)
         except HousekeeperFileMissingError:
             LOG.warning(f"Sample sheet for flow cell {flow_cell_id} not found in Housekeeper")
             return
-        return self.get_valid_sample_sheet_path(sample_sheet_path)
+        if correct_sheet_path := self.get_valid_sample_sheet_path(sample_sheet_path):
+            return correct_sheet_path
+        else:
+            LOG.warning(
+                f"Sample sheet for flow cell {flow_cell_id} in Housekeeper is not valid. "
+                f"Deleting invalid sample sheet from Housekeeper"
+            )
+            delete_file_from_housekeeper(file_path=sample_sheet_path, hk_api=self.hk_api)
 
     def get_sample_sheet_content(self, flow_cell: FlowCellDirectoryData) -> list[list[str]]:
         """Return the sample sheet content for a flow cell."""
diff --git a/cg/meta/demultiplex/housekeeper_storage_functions.py b/cg/meta/demultiplex/housekeeper_storage_functions.py
index a9da2eebe2..df1796a376 100644
--- a/cg/meta/demultiplex/housekeeper_storage_functions.py
+++ b/cg/meta/demultiplex/housekeeper_storage_functions.py
@@ -48,9 +48,9 @@ def store_undetermined_fastq_files(
     flow_cell: FlowCellDirectoryData, hk_api: HousekeeperAPI, store: Store
 ) -> None:
     """Store undetermined fastq files for non-pooled samples in Housekeeper."""
-    non_pooled_lanes_and_samples: list[tuple[int, str]] = (
-        flow_cell.sample_sheet.get_non_pooled_lanes_and_samples()
-    )
+    non_pooled_lanes_and_samples: list[
+        tuple[int, str]
+    ] = flow_cell.sample_sheet.get_non_pooled_lanes_and_samples()
 
     for lane, sample_id in non_pooled_lanes_and_samples:
         undetermined_fastqs: list[Path] = get_undetermined_fastqs(
@@ -176,6 +176,12 @@ def add_and_include_sample_sheet_path_to_housekeeper(
         )
 
 
+def delete_file_from_housekeeper(file_path: Path, hk_api: HousekeeperAPI) -> None:
+    """Delete a file from Housekeeper database and disk given its path."""
+    file: File = hk_api.files(path=file_path.as_posix()).first()
+    hk_api.delete_file(file_id=file.id)
+
+
 def delete_sequencing_data_from_housekeeper(flow_cell_id: str, hk_api: HousekeeperAPI) -> None:
     """Delete FASTQ, SPRING and metadata files associated with a flow cell from Housekeeper."""
     tag_combinations: list[set[str]] = [