diff --git a/cmd/stacker/main.go b/cmd/stacker/main.go
index 5ab577a06..566ba2866 100644
--- a/cmd/stacker/main.go
+++ b/cmd/stacker/main.go
@@ -123,6 +123,8 @@ func main() {
 		&checkCmd,
 	}
 
+	app.DisableSliceFlagSeparator = true
+
 	app.Flags = []cli.Flag{
 		&cli.StringFlag{
 			Name:  "work-dir",
diff --git a/test/basic.bats b/test/basic.bats
index 63258c7d3..c7841090a 100644
--- a/test/basic.bats
+++ b/test/basic.bats
@@ -304,3 +304,15 @@ EOF
     [ ! -f dest/rootfs/favicon.ico ]
     [ ! -d dest/rootfs/stacker ]
 }
+
+@test "commas in substitute flags ok" {
+    cat > stacker.yaml <<EOF
+busybox:
+    from:
+        type: oci
+        url: $BUSYBOX_OCI
+    run: |
+        touch /foo
+EOF
+    stacker build --substitute "a=b,c"
+}