diff --git a/pkg/up/generate.go b/pkg/up/generate.go
index 88216eda9..c41a50c9a 100644
--- a/pkg/up/generate.go
+++ b/pkg/up/generate.go
@@ -17,11 +17,6 @@ type templatePair struct {
 	cloudless bool
 }
 
-func (ctx *Context) Cleanup() {
-	_ = git.RemoveSubmodule("bootstrap")
-	_ = os.RemoveAll("./bootstrap")
-}
-
 func (ctx *Context) Generate() (dir string, err error) {
 	dir, err = os.MkdirTemp("", "sampledir")
 	ctx.dir = dir
diff --git a/pkg/up/prune.go b/pkg/up/prune.go
index 0b0616f57..0ee52c07d 100644
--- a/pkg/up/prune.go
+++ b/pkg/up/prune.go
@@ -38,7 +38,6 @@ func (ctx *Context) Prune() error {
 	}
 
 	_ = os.RemoveAll("./terraform/apps")
-	ctx.Cleanup()
 
 	return git.Sync(repoRoot, "Post-setup resource cleanup", true)
 }