diff --git a/apiv2/db_import/common/config.py b/apiv2/db_import/common/config.py
index d838f78e1..04424da2e 100644
--- a/apiv2/db_import/common/config.py
+++ b/apiv2/db_import/common/config.py
@@ -54,21 +54,27 @@ def load_deposition_map(self) -> None:
             self.deposition_map[item.id] = item
 
     @lru_cache  # noqa
-    def get_alignment_by_path(self, path: str) -> int | None:
+    def get_alignment_by_path(self, path: str, run_id: int) -> int | None:
         session = self.get_db_session()
-        for item in session.scalars(
-            sa.select(models.Alignment).where(models.Alignment.s3_alignment_metadata == path),
-        ).all():
+        where_clauses = [
+            models.Alignment.run_id == run_id,
+            models.Alignment.s3_alignment_metadata == path,
+        ]
+        for item in session.scalars(sa.select(models.Alignment).where(sa.and_(*where_clauses))).all():
             return item.id
 
     @lru_cache  # noqa
-    def get_tiltseries_by_path(self, path: str) -> int | None:
+    def get_tiltseries_by_path(self, path: str, run_id: int) -> int | None:
         session = self.get_db_session()
         # '_' is a wildcard character in sql LIKE queries, so we need to escape them!
         escaped_path = os.path.dirname(path).replace("_", "\\_")
         path = os.path.join(self.s3_prefix, escaped_path, "%")
         try:
-            item = session.scalars(sa.select(models.Tiltseries).where(models.Tiltseries.s3_mrc_file.like(path))).one()
+            where_clauses = [
+                models.Tiltseries.run_id == run_id,
+                models.Tiltseries.s3_mrc_file.like(path),
+            ]
+            item = session.scalars(sa.select(models.Tiltseries).where(sa.and_(*where_clauses))).one()
             return item.id
         except NoResultFound:
             # We have a few runs that (erroneously) are missing tiltseries.
diff --git a/apiv2/db_import/importers/alignment.py b/apiv2/db_import/importers/alignment.py
index 404195c74..986c324bd 100644
--- a/apiv2/db_import/importers/alignment.py
+++ b/apiv2/db_import/importers/alignment.py
@@ -46,12 +46,16 @@ class AlignmentItem(ItemDBImporter):
     model_class = models.Alignment
 
     def load_computed_fields(self):
+        run_id = self.input_data["run"].id
         if self.model_args["alignment_method"] == "undefined":
             self.model_args["alignment_method"] = None
         self.model_args["s3_alignment_metadata"] = self.get_s3_url(self.input_data["file"])
         self.model_args["https_alignment_metadata"] = self.get_https_url(self.input_data["file"])
         if self.input_data.get("tiltseries_path"):
-            self.model_args["tiltseries_id"] = self.config.get_tiltseries_by_path(self.input_data["tiltseries_path"])
+            self.model_args["tiltseries_id"] = self.config.get_tiltseries_by_path(
+                self.input_data["tiltseries_path"],
+                run_id,
+            )
         self.model_args["run_id"] = self.input_data["run"].id
 
 
diff --git a/apiv2/db_import/importers/annotation.py b/apiv2/db_import/importers/annotation.py
index 7a44fd552..0d45bdee6 100644
--- a/apiv2/db_import/importers/annotation.py
+++ b/apiv2/db_import/importers/annotation.py
@@ -75,7 +75,9 @@ def load_computed_fields(self):
         self.model_args["annotation_shape_id"] = self.input_data["annotation_shape"].id
         self.model_args["tomogram_voxel_spacing_id"] = self.input_data["tomogram_voxel_spacing"].id
         if alignment_path:
-            self.model_args["alignment_id"] = self.config.get_alignment_by_path(alignment_path)
+            self.model_args["alignment_id"] = self.config.get_alignment_by_path(
+                alignment_path, self.input_data["run"].id,
+            )
         self.model_args["source"] = self.calculate_source()
         self.model_args["s3_path"] = self.get_s3_url(self.input_data["path"])
         self.model_args["https_path"] = self.get_https_url(self.input_data["path"])
diff --git a/apiv2/db_import/importers/tomogram.py b/apiv2/db_import/importers/tomogram.py
index 5639a9630..395a14ffb 100644
--- a/apiv2/db_import/importers/tomogram.py
+++ b/apiv2/db_import/importers/tomogram.py
@@ -53,10 +53,11 @@ def generate_neuroglancer_data(self, path) -> str | None:
 
     def load_computed_fields(self):
         https_prefix = self.config.https_prefix
+        run_id = self.input_data["run"].id
         extra_data = {
             "ctf_corrected": bool(self.input_data.get("ctf_corrected")),
             "tomogram_voxel_spacing_id": self.input_data["tomogram_voxel_spacing"].id,
-            "run_id": self.input_data["run"].id,
+            "run_id": run_id,
             "fiducial_alignment_status": normalize_fiducial_alignment(
                 self.input_data.get("fiducial_alignment_status", False),
             ),
@@ -68,7 +69,7 @@ def load_computed_fields(self):
             "https_mrc_file": self.get_https_url(self.input_data["mrc_file"]),
             # TODO: Add alignment_id once we have an alignment importer.
             "alignment_id": self.config.get_alignment_by_path(
-                self.get_s3_url(self.input_data["alignment_metadata_path"]),
+                self.get_s3_url(self.input_data["alignment_metadata_path"]), run_id,
             ),
             "key_photo_url": None,
             "key_photo_thumbnail_url": None,