diff --git a/libindex/libindex.go b/libindex/libindex.go
index ff46fc0ba..f359f535f 100644
--- a/libindex/libindex.go
+++ b/libindex/libindex.go
@@ -21,7 +21,7 @@ import (
 	"github.com/quay/claircore/internal/indexer/controller"
 )
 
-const versionMagic = "libindex number: 1\n"
+const versionMagic = "libindex number: 2\n"
 
 // Libindex implements the method set for scanning and indexing a Manifest.
 type Libindex struct {
diff --git a/libindex/migrations/migration3.go b/libindex/migrations/migration3.go
new file mode 100644
index 000000000..44843c5cc
--- /dev/null
+++ b/libindex/migrations/migration3.go
@@ -0,0 +1,19 @@
+package migrations
+
+const (
+	// This migration truncates the manifest_index and scanned_manifest tables
+	// and adds a unique index to manifest_index. This is required since the
+	// manifest_index table currently bloats with duplicate records.
+	//
+	// After this migration is complete manifests will need to be re-indexed
+	// for notifications on these manifests to work correctly.
+	//
+	// Index reports will still be served without a re-index being necessary.
+	migration3 = `
+LOCK manifest_index;
+LOCK scanned_manifest;
+TRUNCATE manifest_index;
+TRUNCATE scanned_manifest;
+CREATE UNIQUE INDEX manifest_index_unique ON manifest_index (package_id, COALESCE(dist_id, 0), COALESCE(repo_id, 0), manifest_id);
+`
+)
diff --git a/libindex/migrations/migrations.go b/libindex/migrations/migrations.go
index df74ad352..72b3fe829 100644
--- a/libindex/migrations/migrations.go
+++ b/libindex/migrations/migrations.go
@@ -25,4 +25,11 @@ var Migrations = []migrate.Migration{
 			return err
 		},
 	},
+	{
+		ID: 3,
+		Up: func(tx *sql.Tx) error {
+			_, err := tx.Exec(migration3)
+			return err
+		},
+	},
 }