diff --git a/go/ql/integration-tests/mixed-layout/diagnostics.expected b/go/ql/integration-tests/mixed-layout/diagnostics.expected
index bbbdd515d68..31e7dd57fcc 100644
--- a/go/ql/integration-tests/mixed-layout/diagnostics.expected
+++ b/go/ql/integration-tests/mixed-layout/diagnostics.expected
@@ -13,7 +13,7 @@
   }
 }
 {
-  "markdownMessage": "Go files were found outside of the Go modules corresponding to these `go.mod` files.\n\n`workspace/subdir/go.mod`, `module/go.mod`",
+  "markdownMessage": "Go files were found outside of the Go modules corresponding to these `go.mod` files.\n\n`workspace/subdir/go.mod`, `module/go.mod`, `no-packages/go.mod`",
   "severity": "note",
   "source": {
     "extractorName": "go",
@@ -26,3 +26,17 @@
     "telemetry": true
   }
 }
+{
+  "markdownMessage": "The following 1 Go project could not be extracted successfully:\n\n`no-packages`\n",
+  "severity": "warning",
+  "source": {
+    "extractorName": "go",
+    "id": "go/autobuilder/extraction-failed-for-project",
+    "name": "Unable to extract some Go projects"
+  },
+  "visibility": {
+    "cliSummaryTable": true,
+    "statusPage": true,
+    "telemetry": true
+  }
+}
diff --git a/go/ql/integration-tests/mixed-layout/src/no-packages/README.md b/go/ql/integration-tests/mixed-layout/src/no-packages/README.md
new file mode 100644
index 00000000000..ac54bf0fb4f
--- /dev/null
+++ b/go/ql/integration-tests/mixed-layout/src/no-packages/README.md
@@ -0,0 +1,3 @@
+This folder contains a Go module and a Go source file, but no packages will be extracted due to build constraints.
+
+Overall extraction should still succeed, because there are other Go modules in this workspace for which we are able to extract files.
diff --git a/go/ql/integration-tests/mixed-layout/src/no-packages/go.mod b/go/ql/integration-tests/mixed-layout/src/no-packages/go.mod
new file mode 100644
index 00000000000..a335389058a
--- /dev/null
+++ b/go/ql/integration-tests/mixed-layout/src/no-packages/go.mod
@@ -0,0 +1,5 @@
+go 1.22
+
+toolchain go1.22.0
+
+module module
diff --git a/go/ql/integration-tests/mixed-layout/src/no-packages/package_test.go b/go/ql/integration-tests/mixed-layout/src/no-packages/package_test.go
new file mode 100644
index 00000000000..404465a7a20
--- /dev/null
+++ b/go/ql/integration-tests/mixed-layout/src/no-packages/package_test.go
@@ -0,0 +1,11 @@
+//go:build unit
+
+package subdir
+
+import (
+	"fmt"
+)
+
+func test() {
+	fmt.Print("Hello world")
+}