diff --git a/database/migrations/000088_fix_rule_instance_id.down.sql b/database/migrations/000088_fix_rule_instance_id.down.sql
new file mode 100644
index 0000000000..ccfaa840bd
--- /dev/null
+++ b/database/migrations/000088_fix_rule_instance_id.down.sql
@@ -0,0 +1,15 @@
+-- Copyright 2024 Stacklok, Inc
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--      http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+-- Nothing to undo
\ No newline at end of file
diff --git a/database/migrations/000088_fix_rule_instance_id.up.sql b/database/migrations/000088_fix_rule_instance_id.up.sql
new file mode 100644
index 0000000000..c36e5ad2b4
--- /dev/null
+++ b/database/migrations/000088_fix_rule_instance_id.up.sql
@@ -0,0 +1,93 @@
+-- Copyright 2024 Stacklok, Inc
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--      http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+BEGIN;
+
+UPDATE rule_evaluations
+SET rule_instance_id = ri.id
+FROM rule_instances AS ri
+WHERE rule_evaluations.profile_id = ri.profile_id
+    AND rule_evaluations.rule_name = ri.name
+    AND rule_evaluations.rule_type_id = ri.rule_type_id
+    AND rule_evaluations.entity = ri.entity_type;
+
+-- the previous migration may have flagged some rows as migrated which should
+-- not have been migrated. Redo them.
+
+UPDATE rule_evaluations AS re
+SET migrated = TRUE
+FROM evaluation_rule_entities AS ere
+WHERE re.entity = 'pull_request'::entities
+  AND ere.entity_type = 'pull_request'::entities
+  AND ere.pull_request_id = re.pull_request_id
+  AND ere.rule_id = re.rule_instance_id;
+
+UPDATE rule_evaluations AS re
+SET migrated = TRUE
+FROM evaluation_rule_entities AS ere
+WHERE re.entity = 'artifact'::entities
+  AND ere.entity_type = 'artifact'::entities
+  AND ere.artifact_id = re.artifact_id
+  AND ere.rule_id = re.rule_instance_id;
+
+UPDATE rule_evaluations AS re
+SET migrated = TRUE
+FROM evaluation_rule_entities AS ere
+WHERE re.entity = 'repository'::entities
+  AND ere.entity_type = 'repository'::entities
+  AND ere.repository_id = re.repository_id
+  AND ere.rule_id = re.rule_instance_id;
+
+-- ensure that any non-migrated rows are set to false
+
+UPDATE rule_evaluations
+SET migrated = FALSE
+WHERE entity = 'artifact'::entities
+AND id IN (
+    SELECT re.id FROM rule_evaluations AS re
+    LEFT JOIN evaluation_rule_entities AS ere
+        ON  re.artifact_id = ere.artifact_id
+        AND re.rule_instance_id = ere.rule_id
+        AND re.entity = 'artifact'::entities
+        AND ere.entity_type = 'artifact'::entities
+    WHERE ere.id IS NULL
+);
+
+UPDATE rule_evaluations
+SET migrated = FALSE
+WHERE entity = 'pull_request'::entities
+AND id IN (
+    SELECT re.id FROM rule_evaluations AS re
+    LEFT JOIN evaluation_rule_entities AS ere
+        ON  re.pull_request_id = ere.pull_request_id
+        AND re.rule_instance_id = ere.rule_id
+        AND re.entity = 'pull_request'::entities
+        AND ere.entity_type = 'pull_request'::entities
+    WHERE ere.id IS NULL
+);
+
+UPDATE rule_evaluations
+SET migrated = FALSE
+WHERE entity = 'repository'::entities
+AND id IN (
+    SELECT re.id FROM rule_evaluations AS re
+    LEFT JOIN evaluation_rule_entities AS ere
+        ON  re.repository_id = ere.repository_id
+        AND re.rule_instance_id = ere.rule_id
+        AND re.entity = 'repository'::entities
+        AND ere.entity_type = 'repository'::entities
+    WHERE ere.id IS NULL
+);
+
+COMMIT;
\ No newline at end of file