diff --git a/go/ql/integration-tests/no-packages-in-any-module/build_environment.expected b/go/ql/integration-tests/no-packages-in-any-module/build_environment.expected
new file mode 100644
index 00000000000..0b225ce0085
--- /dev/null
+++ b/go/ql/integration-tests/no-packages-in-any-module/build_environment.expected
@@ -0,0 +1,5 @@
+{
+  "configuration" : {
+    "go" : { }
+  }
+}
diff --git a/go/ql/integration-tests/no-packages-in-any-module/diagnostics.expected b/go/ql/integration-tests/no-packages-in-any-module/diagnostics.expected
new file mode 100644
index 00000000000..188f3668d7e
--- /dev/null
+++ b/go/ql/integration-tests/no-packages-in-any-module/diagnostics.expected
@@ -0,0 +1,56 @@
+{
+  "markdownMessage": "2 `go.mod` files were found:\n\n`module/go.mod`, `no-packages/go.mod`",
+  "severity": "note",
+  "source": {
+    "extractorName": "go",
+    "id": "go/autobuilder/multiple-go-mod-found-not-nested",
+    "name": "Multiple `go.mod` files found, not all nested under one root `go.mod` file"
+  },
+  "visibility": {
+    "cliSummaryTable": false,
+    "statusPage": false,
+    "telemetry": true
+  }
+}
+{
+  "markdownMessage": "CodeQL was unable to extract any Go files in <test-root-directory>/src/module. If this is unexpected, [specify a custom build command](https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-the-codeql-workflow-for-compiled-languages) that includes one or more `go build` commands to build the `.go` files to be analyzed.",
+  "severity": "warning",
+  "source": {
+    "extractorName": "go",
+    "id": "go/autobuilder/go-files-found-but-not-processed-for-directory",
+    "name": "Go files were found but not processed for a directory"
+  },
+  "visibility": {
+    "cliSummaryTable": true,
+    "statusPage": true,
+    "telemetry": true
+  }
+}
+{
+  "markdownMessage": "CodeQL was unable to extract any Go files in <test-root-directory>/src/no-packages. If this is unexpected, [specify a custom build command](https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-the-codeql-workflow-for-compiled-languages) that includes one or more `go build` commands to build the `.go` files to be analyzed.",
+  "severity": "warning",
+  "source": {
+    "extractorName": "go",
+    "id": "go/autobuilder/go-files-found-but-not-processed-for-directory",
+    "name": "Go files were found but not processed for a directory"
+  },
+  "visibility": {
+    "cliSummaryTable": true,
+    "statusPage": true,
+    "telemetry": true
+  }
+}
+{
+  "markdownMessage": "[Specify a custom build command](https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-the-codeql-workflow-for-compiled-languages) that includes one or more `go build` commands to build the `.go` files to be analyzed.",
+  "severity": "error",
+  "source": {
+    "extractorName": "go",
+    "id": "go/autobuilder/go-files-found-but-not-processed",
+    "name": "Go files were found but not processed"
+  },
+  "visibility": {
+    "cliSummaryTable": true,
+    "statusPage": true,
+    "telemetry": true
+  }
+}
diff --git a/go/ql/integration-tests/no-packages-in-any-module/src/module/go.mod b/go/ql/integration-tests/no-packages-in-any-module/src/module/go.mod
new file mode 100644
index 00000000000..290a5c5c289
--- /dev/null
+++ b/go/ql/integration-tests/no-packages-in-any-module/src/module/go.mod
@@ -0,0 +1,5 @@
+go 1.14
+
+require golang.org/x/net v0.23.0
+
+module module
diff --git a/go/ql/integration-tests/no-packages-in-any-module/src/module/go.sum b/go/ql/integration-tests/no-packages-in-any-module/src/module/go.sum
new file mode 100644
index 00000000000..a8e1b59ae4b
--- /dev/null
+++ b/go/ql/integration-tests/no-packages-in-any-module/src/module/go.sum
@@ -0,0 +1,45 @@
+github.com/yuin/goldmark v1.4.13/go.mod h1:6yULJ656Px+3vBD8DxQVa3kxgyrAnzto9xy5taEt/CY=
+golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
+golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
+golang.org/x/crypto v0.19.0/go.mod h1:Iy9bg/ha4yyC70EfRS8jz+B6ybOBKMaSxLj6P6oBDfU=
+golang.org/x/crypto v0.21.0/go.mod h1:0BP7YvVV9gBbVKyeTG0Gyn+gZm94bibOW5BjDEYAOMs=
+golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4/go.mod h1:jJ57K6gSWd91VN4djpZkiMVwK6gcyfeH4XE8wZrZaV4=
+golang.org/x/mod v0.8.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs=
+golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
+golang.org/x/net v0.0.0-20210226172049-e18ecbb05110/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg=
+golang.org/x/net v0.0.0-20220722155237-a158d28d115b/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c=
+golang.org/x/net v0.6.0/go.mod h1:2Tu9+aMcznHK/AK1HMvgo6xiTLG5rD5rZLDS+rp2Bjs=
+golang.org/x/net v0.10.0/go.mod h1:0qNGK6F8kojg2nk9dLZ2mShWaEBan6FAoqfSigmmuDg=
+golang.org/x/net v0.21.0/go.mod h1:bIjVDfnllIU7BJ2DNgfnXvpSvtn8VRwhlsaeUTyUS44=
+golang.org/x/net v0.23.0 h1:7EYJ93RZ9vYSZAIb2x3lnuvqO5zneoD6IvWjuhfxjTs=
+golang.org/x/net v0.23.0/go.mod h1:JKghWKKOSdJwpW2GEx0Ja7fmaKnMsbu+MWVZTokSYmg=
+golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sync v0.0.0-20220722155255-886fb9371eb4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sync v0.1.0/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.0.0-20220520151302-bc2c85ada10a/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.5.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.8.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.17.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
+golang.org/x/sys v0.18.0 h1:DBdB3niSjOA/O0blCZBqDefyWNYveAYMNF1Wum0DYQ4=
+golang.org/x/sys v0.18.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
+golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
+golang.org/x/term v0.0.0-20210927222741-03fcf44c2211/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8=
+golang.org/x/term v0.5.0/go.mod h1:jMB1sMXY+tzblOD4FWmEbocvup2/aLOaQEp7JmGp78k=
+golang.org/x/term v0.8.0/go.mod h1:xPskH00ivmX89bAKVGSKKtLOWNx2+17Eiy94tnKShWo=
+golang.org/x/term v0.17.0/go.mod h1:lLRBjIVuehSbZlaOtGMbcMncT+aqLLLmKrsjNrUguwk=
+golang.org/x/term v0.18.0/go.mod h1:ILwASektA3OnRv7amZ1xhE/KTR+u50pbXfZ03+6Nx58=
+golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
+golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
+golang.org/x/text v0.3.7/go.mod h1:u+2+/6zg+i71rQMx5EYifcz6MCKuco9NR6JIITiCfzQ=
+golang.org/x/text v0.7.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8=
+golang.org/x/text v0.9.0/go.mod h1:e1OnstbJyHTd6l/uOt8jFFHp6TRDWZR/bV3emEE/zU8=
+golang.org/x/text v0.14.0/go.mod h1:18ZOQIKpY8NJVqYksKHtTdi31H5itFRjB5/qKTNYzSU=
+golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
+golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
+golang.org/x/tools v0.1.12/go.mod h1:hNGJHUnrk76NpqgfD5Aqm5Crs+Hm0VOH/i9J2+nxYbc=
+golang.org/x/tools v0.6.0/go.mod h1:Xwgl3UAJ/d3gWutnCtw505GrjyAbvKui8lOU390QaIU=
+golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
diff --git a/go/ql/integration-tests/no-packages-in-any-module/src/module/test.go b/go/ql/integration-tests/no-packages-in-any-module/src/module/test.go
new file mode 100644
index 00000000000..245f0237cd9
--- /dev/null
+++ b/go/ql/integration-tests/no-packages-in-any-module/src/module/test.go
@@ -0,0 +1,15 @@
+//go:build unit
+
+package subdir
+
+import (
+	"fmt"
+
+	"golang.org/x/net/ipv4"
+)
+
+func test() {
+
+	header := ipv4.Header{}
+	fmt.Print(header.String())
+}
diff --git a/go/ql/integration-tests/no-packages-in-any-module/src/no-packages/go.mod b/go/ql/integration-tests/no-packages-in-any-module/src/no-packages/go.mod
new file mode 100644
index 00000000000..a335389058a
--- /dev/null
+++ b/go/ql/integration-tests/no-packages-in-any-module/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/no-packages-in-any-module/src/no-packages/package_test.go b/go/ql/integration-tests/no-packages-in-any-module/src/no-packages/package_test.go
new file mode 100644
index 00000000000..404465a7a20
--- /dev/null
+++ b/go/ql/integration-tests/no-packages-in-any-module/src/no-packages/package_test.go
@@ -0,0 +1,11 @@
+//go:build unit
+
+package subdir
+
+import (
+	"fmt"
+)
+
+func test() {
+	fmt.Print("Hello world")
+}
diff --git a/go/ql/integration-tests/no-packages-in-any-module/test.py b/go/ql/integration-tests/no-packages-in-any-module/test.py
new file mode 100644
index 00000000000..2b009876f9a
--- /dev/null
+++ b/go/ql/integration-tests/no-packages-in-any-module/test.py
@@ -0,0 +1,2 @@
+def test(codeql, go):
+    codeql.database.create(source_root="src", _assert_failure=True)