diff --git a/go/libraries/doltcore/migrate/transform.go b/go/libraries/doltcore/migrate/transform.go
index 357bea291b..93c253148c 100644
--- a/go/libraries/doltcore/migrate/transform.go
+++ b/go/libraries/doltcore/migrate/transform.go
@@ -481,10 +481,19 @@ func migrateSchema(ctx context.Context, tableName string, existing schema.Schema
 		}
 	}
 
-	if patched {
-		return schema.SchemaFromCols(schema.NewColCollection(cols...))
+	if !patched {
+		return existing, nil
 	}
-	return existing, nil
+
+	sch, err := schema.SchemaFromCols(schema.NewColCollection(cols...))
+	if err != nil {
+		return nil, err
+	}
+
+	if err = sch.SetPkOrdinals(existing.GetPkOrdinals()); err != nil {
+		return nil, err
+	}
+	return sch, nil
 }
 
 func migrateIndexSet(
diff --git a/integration-tests/bats/migrate.bats b/integration-tests/bats/migrate.bats
index 3696927f1a..33f13fdd4f 100644
--- a/integration-tests/bats/migrate.bats
+++ b/integration-tests/bats/migrate.bats
@@ -229,3 +229,22 @@ SQL
     run dolt sql -q "SELECT * FROM t ORDER BY a LIMIT 1" -r csv
     [[ "$output" =~ "h&a,B" ]] || false
 }
+
+@test "migrate: database with inverted primary key order" {
+    dolt sql <<SQL
+CREATE TABLE t (
+    pk2 varchar(20) NOT NULL,
+    pk1 varchar(20) NOT NULL,
+    PRIMARY KEY (pk1, pk2));
+INSERT INTO t (pk2, pk1) VALUES ("z","a"),("y","b"),("x","c");
+SQL
+    dolt commit -Am "added table t"
+
+    run dolt schema show t
+    [[ "$output" =~ "PRIMARY KEY (\`pk1\`,\`pk2\`)" ]] || false
+
+    dolt migrate
+
+    run dolt schema show t
+    [[ "$output" =~ "PRIMARY KEY (\`pk1\`,\`pk2\`)" ]] || false
+}