diff --git a/build/ci.go b/build/ci.go
index e589cd2b40..17071394ac 100644
--- a/build/ci.go
+++ b/build/ci.go
@@ -464,7 +464,7 @@ func doCheckGenerate() {
 
 	for _, mod := range goModules {
 		// Compute the origin hashes of all the files
-		hashes, err := build.HashFolder(mod, []string{"tests/testdata", "build/cache", ".git"})
+		hashes, err := build.HashFolder(mod, []string{"tests/testdata", "build/cache", ".git", ".jj"})
 		if err != nil {
 			log.Fatal("Error computing hashes", "err", err)
 		}
@@ -474,7 +474,7 @@ func doCheckGenerate() {
 		c.Dir = mod
 		build.MustRun(c)
 		// Check if generate file hashes have changed
-		generated, err := build.HashFolder(mod, []string{"tests/testdata", "build/cache", ".git"})
+		generated, err := build.HashFolder(mod, []string{"tests/testdata", "build/cache", ".git", ".jj"})
 		if err != nil {
 			log.Fatalf("Error re-computing hashes: %v", err)
 		}