diff --git a/gazelle/buf/buf_test.go b/gazelle/buf/buf_test.go
index ba43aac..b9c0bcc 100644
--- a/gazelle/buf/buf_test.go
+++ b/gazelle/buf/buf_test.go
@@ -71,6 +71,11 @@ func TestMerge(t *testing.T) {
 	testRunGazelle(t, "v2/merge")
 }
 
+func TestMix(t *testing.T) {
+	t.Parallel()
+	testRunGazelle(t, "mix")
+}
+
 func TestImportResolve(t *testing.T) {
 	t.Parallel()
 	testRunGazelle(t, "imports", "update-repos", "--from_file=buf.work.yaml", "-to_macro=buf_deps.bzl%buf_deps", "-prune")
diff --git a/gazelle/buf/config.go b/gazelle/buf/config.go
index 43a2dba..905e473 100644
--- a/gazelle/buf/config.go
+++ b/gazelle/buf/config.go
@@ -22,6 +22,7 @@ import (
 	"io/fs"
 	"log"
 	"os"
+	"path"
 	"path/filepath"
 	"strconv"
 	"strings"
@@ -85,19 +86,26 @@ func loadConfig(gazelleConfig *config.Config, packageRelativePath string, file *
 	if err != nil {
 		log.Print("error trying to load default config", err)
 	}
+	// log.Println("loadConfig", packageRelativePath)
+	// Two cases where this could be the module root:
+	// 1. If there is a buf.yaml file and no modules are defined.
+	if bufModule != nil {
+		config.Module = bufModule
+		config.BufConfigFile = label.New("", packageRelativePath, bufConfigFile)
+		config.ModuleRoot = len(bufModule.Modules) == 0
+	}
+	// 2. If the ancestor has a v2 buf.yaml file with matching path.
 	if config.Module != nil && config.Module.Version == "v2" {
 		for _, module := range config.Module.Modules {
-			if module.Path == packageRelativePath {
+			if module.Path == "." {
+				module.Path = ""
+			}
+			if path.Join(config.BufConfigFile.Pkg, module.Path) == packageRelativePath {
 				config.ModuleRoot = true
-				config.BufConfigFile = label.New("", "", "buf.yaml") // v2 will always have a buf.yaml at the roor.
 				config.ModuleConfig = &module
 				break
 			}
 		}
-	} else if bufModule != nil {
-		config.Module = bufModule
-		config.ModuleRoot = true
-		config.BufConfigFile = label.New("", packageRelativePath, bufConfigFile)
 	}
 	// When using workspaces, for gazelle to generate accurate proto_library rules
 	// we need add `# gazelle:proto_strip_import_prefix /path` to BUILD file at each module root
diff --git a/gazelle/buf/generate.go b/gazelle/buf/generate.go
index f22f5cd..373a0a8 100644
--- a/gazelle/buf/generate.go
+++ b/gazelle/buf/generate.go
@@ -86,7 +86,7 @@ func generateLintRule(config *Config, target string) *rule.Rule {
 	if config.Module != nil {
 		r.SetAttr("config", config.BufConfigFile.String())
 	}
-	if config.ModuleConfig != nil {
+	if config.ModuleConfig != nil && config.ModuleConfig.Path != "" {
 		r.SetAttr("module", config.ModuleConfig.Path)
 	}
 	return r
@@ -106,7 +106,7 @@ func generateBreakingRule(config *Config, target string) *rule.Rule {
 	if config.Module != nil {
 		r.SetAttr("config", config.BufConfigFile.String())
 	}
-	if config.ModuleConfig != nil {
+	if config.ModuleConfig != nil && config.ModuleConfig.Path != "" {
 		r.SetAttr("module", config.ModuleConfig.Path)
 	}
 	return r
diff --git a/gazelle/buf/testdata/mix/buf.yaml b/gazelle/buf/testdata/mix/buf.yaml
new file mode 100644
index 0000000..b8e8d51
--- /dev/null
+++ b/gazelle/buf/testdata/mix/buf.yaml
@@ -0,0 +1,18 @@
+version: v2
+modules:
+  - path: barapis
+  - path: fooapis
+  - path: petapis
+lint:
+  use:
+    - DEFAULT
+  except:
+    - FIELD_NOT_REQUIRED
+    - PACKAGE_NO_IMPORT_CYCLE
+  disallow_comment_ignores: true
+breaking:
+  use:
+    - FILE
+  except:
+    - EXTENSION_NO_DELETE
+    - FIELD_SAME_DEFAULT
diff --git a/gazelle/buf/testdata/mix/fooapis/BUILD.in b/gazelle/buf/testdata/mix/fooapis/BUILD.in
new file mode 100644
index 0000000..c1d725b
--- /dev/null
+++ b/gazelle/buf/testdata/mix/fooapis/BUILD.in
@@ -0,0 +1 @@
+# gazelle:buf_breaking_against //:against_file
diff --git a/gazelle/buf/testdata/mix/fooapis/BUILD.out b/gazelle/buf/testdata/mix/fooapis/BUILD.out
new file mode 100644
index 0000000..5b16619
--- /dev/null
+++ b/gazelle/buf/testdata/mix/fooapis/BUILD.out
@@ -0,0 +1,11 @@
+load("@rules_buf//buf:defs.bzl", "buf_breaking_test")
+
+# gazelle:buf_breaking_against //:against_file
+
+buf_breaking_test(
+    name = "buf_breaking",
+    against = "//:against_file",
+    config = "//:buf.yaml",
+    module = "fooapis",
+    targets = ["//fooapis/foo/v1:foo_v1_proto"],
+)
diff --git a/gazelle/buf/testdata/mix/fooapis/foo/v1/BUILD.in b/gazelle/buf/testdata/mix/fooapis/foo/v1/BUILD.in
new file mode 100644
index 0000000..e69de29
diff --git a/gazelle/buf/testdata/mix/fooapis/foo/v1/BUILD.out b/gazelle/buf/testdata/mix/fooapis/foo/v1/BUILD.out
new file mode 100644
index 0000000..91fb131
--- /dev/null
+++ b/gazelle/buf/testdata/mix/fooapis/foo/v1/BUILD.out
@@ -0,0 +1,16 @@
+load("@rules_proto//proto:defs.bzl", "proto_library")
+load("@rules_buf//buf:defs.bzl", "buf_lint_test")
+
+proto_library(
+    name = "foo_v1_proto",
+    srcs = ["foo.proto"],
+    strip_import_prefix = "/fooapis",
+    visibility = ["//visibility:public"],
+)
+
+buf_lint_test(
+    name = "foo_v1_proto_lint",
+    config = "//:buf.yaml",
+    module = "fooapis",
+    targets = [":foo_v1_proto"],
+)
diff --git a/gazelle/buf/testdata/mix/fooapis/foo/v1/foo.proto b/gazelle/buf/testdata/mix/fooapis/foo/v1/foo.proto
new file mode 100644
index 0000000..403aebb
--- /dev/null
+++ b/gazelle/buf/testdata/mix/fooapis/foo/v1/foo.proto
@@ -0,0 +1,5 @@
+syntax = "proto3";
+
+package foo.v1;
+
+message Foo {}
diff --git a/gazelle/buf/testdata/mix/petapis/BUILD.in b/gazelle/buf/testdata/mix/petapis/BUILD.in
new file mode 100644
index 0000000..c1d725b
--- /dev/null
+++ b/gazelle/buf/testdata/mix/petapis/BUILD.in
@@ -0,0 +1 @@
+# gazelle:buf_breaking_against //:against_file
diff --git a/gazelle/buf/testdata/mix/petapis/BUILD.out b/gazelle/buf/testdata/mix/petapis/BUILD.out
new file mode 100644
index 0000000..a38cc63
--- /dev/null
+++ b/gazelle/buf/testdata/mix/petapis/BUILD.out
@@ -0,0 +1,11 @@
+load("@rules_buf//buf:defs.bzl", "buf_breaking_test")
+
+# gazelle:buf_breaking_against //:against_file
+
+buf_breaking_test(
+    name = "buf_breaking",
+    against = "//:against_file",
+    config = "//:buf.yaml",
+    module = "petapis",
+    targets = ["//petapis/pets/v1:pets_v1_proto"],
+)
diff --git a/gazelle/buf/testdata/mix/petapis/pets/v1/BUILD.in b/gazelle/buf/testdata/mix/petapis/pets/v1/BUILD.in
new file mode 100644
index 0000000..e69de29
diff --git a/gazelle/buf/testdata/mix/petapis/pets/v1/BUILD.out b/gazelle/buf/testdata/mix/petapis/pets/v1/BUILD.out
new file mode 100644
index 0000000..4c6f8c3
--- /dev/null
+++ b/gazelle/buf/testdata/mix/petapis/pets/v1/BUILD.out
@@ -0,0 +1,17 @@
+load("@rules_proto//proto:defs.bzl", "proto_library")
+load("@rules_buf//buf:defs.bzl", "buf_lint_test")
+
+proto_library(
+    name = "pets_v1_proto",
+    srcs = ["pets.proto"],
+    strip_import_prefix = "/petapis",
+    visibility = ["//visibility:public"],
+    deps = ["//fooapis/foo/v1:foo_v1_proto"],
+)
+
+buf_lint_test(
+    name = "pets_v1_proto_lint",
+    config = "//:buf.yaml",
+    module = "petapis",
+    targets = [":pets_v1_proto"],
+)
diff --git a/gazelle/buf/testdata/mix/petapis/pets/v1/pets.proto b/gazelle/buf/testdata/mix/petapis/pets/v1/pets.proto
new file mode 100644
index 0000000..ba7c841
--- /dev/null
+++ b/gazelle/buf/testdata/mix/petapis/pets/v1/pets.proto
@@ -0,0 +1,9 @@
+syntax = "proto3";
+
+package pets.v1;
+
+import "foo/v1/foo.proto";
+
+message Pet {
+  foo.v1.Foo foo = 1;
+}
diff --git a/gazelle/buf/testdata/mix/v1/BUILD.in b/gazelle/buf/testdata/mix/v1/BUILD.in
new file mode 100644
index 0000000..e69de29
diff --git a/gazelle/buf/testdata/mix/v1/BUILD.out b/gazelle/buf/testdata/mix/v1/BUILD.out
new file mode 100644
index 0000000..e69de29
diff --git a/gazelle/buf/testdata/mix/v1/buf.yaml b/gazelle/buf/testdata/mix/v1/buf.yaml
new file mode 100644
index 0000000..1a51945
--- /dev/null
+++ b/gazelle/buf/testdata/mix/v1/buf.yaml
@@ -0,0 +1,7 @@
+version: v1
+breaking:
+  use:
+    - FILE
+lint:
+  use:
+    - DEFAULT
diff --git a/gazelle/buf/testdata/mix/v1/zap/v1/BUILD.in b/gazelle/buf/testdata/mix/v1/zap/v1/BUILD.in
new file mode 100644
index 0000000..f4bd97d
--- /dev/null
+++ b/gazelle/buf/testdata/mix/v1/zap/v1/BUILD.in
@@ -0,0 +1,9 @@
+load("@rules_proto//proto:defs.bzl", "proto_library")
+load("@rules_buf//buf:defs.bzl", "buf_lint_test")
+
+proto_library(
+    name = "zap_proto",
+    srcs = ["zap.proto"],
+    visibility = ["//visibility:public"],
+)
+
diff --git a/gazelle/buf/testdata/mix/v1/zap/v1/BUILD.out b/gazelle/buf/testdata/mix/v1/zap/v1/BUILD.out
new file mode 100644
index 0000000..41bc718
--- /dev/null
+++ b/gazelle/buf/testdata/mix/v1/zap/v1/BUILD.out
@@ -0,0 +1,15 @@
+load("@rules_proto//proto:defs.bzl", "proto_library")
+load("@rules_buf//buf:defs.bzl", "buf_lint_test")
+
+proto_library(
+    name = "zap_proto",
+    srcs = ["zap.proto"],
+    strip_import_prefix = "/v1",
+    visibility = ["//visibility:public"],
+)
+
+buf_lint_test(
+    name = "zap_proto_lint",
+    config = "//v1:buf.yaml",
+    targets = [":zap_proto"],
+)
diff --git a/gazelle/buf/testdata/mix/v1/zap/v1/zap.proto b/gazelle/buf/testdata/mix/v1/zap/v1/zap.proto
new file mode 100644
index 0000000..e69de29
diff --git a/gazelle/buf/testdata/mix/v2/BUILD.in b/gazelle/buf/testdata/mix/v2/BUILD.in
new file mode 100644
index 0000000..e69de29
diff --git a/gazelle/buf/testdata/mix/v2/BUILD.out b/gazelle/buf/testdata/mix/v2/BUILD.out
new file mode 100644
index 0000000..e69de29
diff --git a/gazelle/buf/testdata/mix/v2/buf.yaml b/gazelle/buf/testdata/mix/v2/buf.yaml
new file mode 100644
index 0000000..6fe9ec4
--- /dev/null
+++ b/gazelle/buf/testdata/mix/v2/buf.yaml
@@ -0,0 +1,14 @@
+version: v2
+lint:
+  use:
+    - DEFAULT
+  except:
+    - FIELD_NOT_REQUIRED
+    - PACKAGE_NO_IMPORT_CYCLE
+  disallow_comment_ignores: true
+breaking:
+  use:
+    - FILE
+  except:
+    - EXTENSION_NO_DELETE
+    - FIELD_SAME_DEFAULT
diff --git a/gazelle/buf/testdata/mix/v2/tap/v1/BUILD.in b/gazelle/buf/testdata/mix/v2/tap/v1/BUILD.in
new file mode 100644
index 0000000..737aaf1
--- /dev/null
+++ b/gazelle/buf/testdata/mix/v2/tap/v1/BUILD.in
@@ -0,0 +1,9 @@
+load("@rules_proto//proto:defs.bzl", "proto_library")
+load("@rules_buf//buf:defs.bzl", "buf_lint_test")
+
+proto_library(
+    name = "tap_proto",
+    srcs = ["tap.proto"],
+    visibility = ["//visibility:public"],
+)
+
diff --git a/gazelle/buf/testdata/mix/v2/tap/v1/BUILD.out b/gazelle/buf/testdata/mix/v2/tap/v1/BUILD.out
new file mode 100644
index 0000000..eaa3497
--- /dev/null
+++ b/gazelle/buf/testdata/mix/v2/tap/v1/BUILD.out
@@ -0,0 +1,15 @@
+load("@rules_proto//proto:defs.bzl", "proto_library")
+load("@rules_buf//buf:defs.bzl", "buf_lint_test")
+
+proto_library(
+    name = "tap_proto",
+    srcs = ["tap.proto"],
+    strip_import_prefix = "/v2",
+    visibility = ["//visibility:public"],
+)
+
+buf_lint_test(
+    name = "tap_proto_lint",
+    config = "//v2:buf.yaml",
+    targets = [":tap_proto"],
+)
diff --git a/gazelle/buf/testdata/mix/v2/tap/v1/tap.proto b/gazelle/buf/testdata/mix/v2/tap/v1/tap.proto
new file mode 100644
index 0000000..e69de29