diff --git a/tools/override-generator/main.go b/tools/override-generator/main.go
index b93fa7e..c0c2aa4 100644
--- a/tools/override-generator/main.go
+++ b/tools/override-generator/main.go
@@ -31,18 +31,15 @@
 
 // attribute constants that are used multiple times.
 const (
-	_buildFileGenerationAttr = "build_file_generation"
-	_buildFileProtoModeAttr  = "build_file_proto_mode"
-	_patchArgsAttr           = "patch_args"
-	_buildDirectivesAttr     = "build_directives"
-	_directivesAttr          = "directives"
+	_buildFileGenerationAttr        = "build_file_generation"
+	_buildFileProtoModeAttr         = "build_file_proto_mode"
+	_patchArgsAttr                  = "patch_args"
+	_buildDirectivesAttr            = "build_directives"
+	_directivesAttr                 = "directives"
+	_buildFileProtoModeDefault      = "default"
+	_buildFileGenerationModeDefault = "auto"
 )
 
-var _defaultValues = map[string]string{
-	_buildFileGenerationAttr: "auto",
-	_buildFileProtoModeAttr:  "default",
-}
-
 var _mapAttrToOverride = map[string]string{
 	_buildDirectivesAttr:     _gazelleOverride,
 	_buildFileGenerationAttr: _gazelleOverride,
@@ -66,6 +63,9 @@
 	defName         string
 	outputFile      string
 	gazelleRepoName string
+
+	defaultBuildFileGeneration string
+	defaultBuildFileProtoMode  string
 }
 
 func main() {
@@ -91,6 +91,8 @@
 	flag.StringVar(&a.defName, "def_name", "", "name of the macro definition")
 	flag.StringVar(&a.outputFile, "output", "", "path to the output file")
 	flag.StringVar(&a.gazelleRepoName, "gazelle_repo_name", "@bazel_gazelle", "name of the gazelle repo to load go_deps, (default: @bazel_gazelle)")
+	flag.StringVar(&a.defaultBuildFileGeneration, "default_build_file_generation", "auto", "the default value for build_file_generation attribute")
+	flag.StringVar(&a.defaultBuildFileProtoMode, "default_build_file_proto_mode", "default", "the default value for build_file_proto_mode attribute")
 	flag.Parse(osArgs)
 
 	if a.macroPath != "" && a.workspace != "" {
@@ -137,7 +139,7 @@
 	// will be deterministic.
 	for _, r := range repos {
 		if r.Kind() == "go_repository" {
-			repoOverrides := goRepositoryToOverrideSet(r)
+			repoOverrides := goRepositoryToOverrideSet(r, a.defaultBuildFileGeneration, a.defaultBuildFileProtoMode)
 			outputOverrides = append(outputOverrides, setToOverridesSlice(repoOverrides)...)
 		}
 	}
@@ -162,7 +164,7 @@
 	return nil
 }
 
-func goRepositoryToOverrideSet(r *rule.Rule) overrideSet {
+func goRepositoryToOverrideSet(r *rule.Rule, defaultBuildFileGeneration, defaultBuildFileProtoMode string) overrideSet {
 	// each repo has its own override set, and can't have multiple
 	// duplicate overrides. This set is created to be populated and read
 	set := make(overrideSet)
@@ -176,7 +178,7 @@
 		}
 
 		attrValue := r.Attr(attr)
-		if attrValue == nil || attr == _buildFileProtoModeAttr {
+		if attrValue == nil || attr == _buildFileProtoModeAttr || attr == _buildFileGenerationAttr {
 			continue
 		}
 
@@ -194,10 +196,6 @@
 			attr = k
 		}
 
-		if def, ok := _defaultValues[attr]; def == r.AttrString(attr) && ok {
-			continue
-		}
-
 		if val != nil {
 			switch v := val.(type) {
 			case *build.StringExpr:
@@ -216,31 +214,86 @@
 		set[kind] = override
 	}
 
-	// Since "build_file_proto_mode" is added to the "directives", we need
-	// to run it after the fact to make sure that "directives" is set.
-	applyBuildFileProtoMode(r, set)
+	// If the user default doesn't match the global default, but there's a gazelle override, we need to still apply
+	// it to the individual overrides.
+	// Also, since "build_file_proto_mode" is added to the "directives", we need
+	// to apply it last to make sure "directives" is set.
+	applyBuildFileGeneration(r, set, defaultBuildFileGeneration)
+	applyBuildFileProtoMode(r, set, defaultBuildFileProtoMode, defaultBuildFileGeneration)
 	return set
 }
 
-func applyBuildFileProtoMode(r *rule.Rule, set overrideSet) {
-	if r.Attr(_buildFileProtoModeAttr) == nil {
+func applyBuildFileGeneration(r *rule.Rule, set overrideSet, userDefaultGeneration string) {
+	ruleGeneration := r.AttrString(_buildFileGenerationAttr)
+	o, ok := set[_gazelleOverride]
+	if !ok {
+	 	if ruleGeneration == "" || ruleGeneration == userDefaultGeneration {
+			return
+		}
+		set[_gazelleOverride] = newGenerationOverride(userDefaultGeneration)
 		return
 	}
 
-	if def, ok := _defaultValues[_buildFileProtoModeAttr]; def == r.AttrString(_buildFileProtoModeAttr) && ok {
+	if ruleGeneration == "" {
+		ruleGeneration = userDefaultGeneration
+	}
+
+	if ruleGeneration == _buildFileGenerationModeDefault {
 		return
 	}
 
-	directive := "gazelle:proto " + r.AttrString(_buildFileProtoModeAttr)
-	kind := _gazelleOverride
-	override := rule.NewRule(kind, "")
-	if o, ok := set[kind]; ok {
-		override = o
+	o.SetAttr(_buildFileGenerationAttr, ruleGeneration)
+	set[_gazelleOverride] = o
+	return
+}
+
+
+func newGenerationOverride(userDefaultGeneration string) *rule.Rule {
+	override := rule.NewRule(_gazelleOverride, "")
+	override.SetAttr(_buildFileGenerationAttr, userDefaultGeneration)
+	return override
+}
+
+func applyBuildFileProtoMode(r *rule.Rule, set overrideSet, userDefaultProtoMode, userDefaultGeneration string) {
+	protoMode := r.AttrString(_buildFileProtoModeAttr)
+
+	// If the gazelle_override doesn't exist. We only need to apply the proto mode
+	// if it does not match the user default proto mode.
+	gazelleOverride, ok := set[_gazelleOverride]
+	if !ok {
+		if protoMode == "" || protoMode == userDefaultProtoMode {
+			return
+		}
+		set[_gazelleOverride] = newProtoOverride(protoMode, userDefaultGeneration)
+		return
 	}
-	directives := override.AttrStrings(_directivesAttr)
+
+	// If the gazelle_override exists, we need to apply the proto mode if the user default
+	// or the provided value doesn't match the tag default.
+	if protoMode == "" {
+		protoMode = userDefaultProtoMode
+	}
+
+	if protoMode == _buildFileProtoModeDefault {
+		return
+	}
+
+	directive := "gazelle:proto " + protoMode
+	directives := gazelleOverride.AttrStrings(_directivesAttr)
 	directives = append(directives, directive)
+	gazelleOverride.SetAttr(_directivesAttr, directives)
+	set[_gazelleOverride] = gazelleOverride
+	return
+}
+
+func newProtoOverride(protoMode, userDefaultGeneration string) *rule.Rule {
+	override := rule.NewRule(_gazelleOverride, "")
+	directives := []string{"gazelle:proto " + protoMode}
 	override.SetAttr(_directivesAttr, directives)
-	set[kind] = override
+	if userDefaultGeneration != _buildFileGenerationModeDefault {
+		override.SetAttr(_buildFileGenerationAttr, userDefaultGeneration)
+	}
+	return override
 }
 
 func setPatchArgs(patchArgs []string, override *rule.Rule) {
diff --git a/tools/override-generator/main_test.go b/tools/override-generator/main_test.go
index 6eed305..617fae3 100644
--- a/tools/override-generator/main_test.go
+++ b/tools/override-generator/main_test.go
@@ -170,8 +170,197 @@
 			}
 
 			args := &mainArgs{
-				workspace:  testWorkspace,
-				outputFile: filepath.Join(w, "output.bzl"),
+				workspace:                  testWorkspace,
+				outputFile:                 filepath.Join(w, "output.bzl"),
+				defaultBuildFileGeneration: "auto",
+				defaultBuildFileProtoMode:  "default",
+			}
+
+			if err := run(*args, io.Discard); err != nil {
+				t.Errorf("run() error = %v, want no error", err)
+			}
+
+			if tt.want == "" {
+				return
+			}
+
+			content, err := os.ReadFile(args.outputFile)
+			if err != nil {
+				t.Errorf("error reading output file: %v", err)
+			}
+
+			if !isEqualContent(string(content), tt.want) {
+				fmt.Fprintf(os.Stderr, "output = %v, want %v", string(content), tt.want)
+				t.Errorf("output = %v, want %v", string(content), tt.want)
+			}
+		})
+	}
+}
+
+func TestBzlmodOverrideNewDefaults(t *testing.T) {
+	tests := []struct {
+		name string
+		give string
+		want string
+	}{
+		{
+			name: "simple no override",
+			give: `load("@bazel_gazelle//:deps.bzl", "go_repository")
+
+			go_repository(
+				name = "com_github_apache_thrift",
+				build_file_generation = "on",
+				build_file_proto_mode = "disable",
+				importpath = "github.com/apache/thrift",
+				sum = "h1:cMd2aj52n+8VoAtvSvLn4kDC3aZ6IAkBuqWQ2IDu7wo=",
+				version = "v0.17.0",
+			)`,
+			want: "",
+		},
+		{
+			name: "simple override",
+			give: `load("@bazel_gazelle//:deps.bzl", "go_repository")
+
+			go_repository(
+				name = "com_github_apache_thrift",
+				build_extra_args = ["-go_naming_convention_external=go_default_library"],
+				build_file_generation = "on",
+				build_file_proto_mode = "disable_global",
+				importpath = "github.com/apache/thrift",
+				sum = "h1:cMd2aj52n+8VoAtvSvLn4kDC3aZ6IAkBuqWQ2IDu7wo=",
+				version = "v0.17.0",
+			)`,
+			want: `go_deps = use_extension("//:extensions.bzl", "go_deps")
+
+			go_deps.gazelle_override(
+				build_extra_args = ["-go_naming_convention_external=go_default_library"],
+				build_file_generation = "on",
+				directives = ["gazelle:proto disable_global"],
+				path = "github.com/apache/thrift",
+			)`,
+		},
+		{
+			name: "module override and gazelle",
+			give: `load("@bazel_gazelle//:deps.bzl", "go_repository")
+
+			go_repository(
+				name = "com_github_bazelbuild_bazel_watcher",
+				build_extra_args = ["-go_naming_convention_external=go_default_library"],
+				build_file_generation = "off",  # keep
+				build_file_proto_mode = "disable",
+				importpath = "github.com/bazelbuild/bazel-watcher",
+				patch_args = ["-p1"],
+				patches = [
+					# Remove it after they release this PR https://github.com/bazelbuild/bazel-watcher/pull/627
+					"//patches:com_github_bazelbuild_bazel_watcher-go-embed.patch",
+				],
+				sum = "h1:EfJzkMxJuNBGMVdEvkhiW7pAMwhaegbmAMaFCjLjyTw=",
+				version = "v0.23.7",
+			)`,
+			want: `go_deps = use_extension("//:extensions.bzl", "go_deps")
+
+			go_deps.gazelle_override(
+				build_extra_args = ["-go_naming_convention_external=go_default_library"],
+				build_file_generation = "off",
+				directives = ["gazelle:proto disable"],
+				path = "github.com/bazelbuild/bazel-watcher",
+			)
+
+			go_deps.module_override(
+				patch_strip = 1,
+				patches = [
+					# Remove it after they release this PR https://github.com/bazelbuild/bazel-watcher/pull/627
+					"//patches:com_github_bazelbuild_bazel_watcher-go-embed.patch",
+				],
+				path = "github.com/bazelbuild/bazel-watcher",
+			)`,
+		},
+		{
+			name: "directives and proto args",
+			give: `go_repository(
+				name = "com_github_clickhouse_clickhouse_go_v2",
+				build_directives = [
+					"gazelle:resolve go github.com/ClickHouse/clickhouse-go/v2/external @com_github_clickhouse_clickhouse_go_v2//external",
+				],
+				build_extra_args = ["-go_naming_convention_external=go_default_library"],
+				build_file_generation = "auto",
+				build_file_proto_mode = "disable",
+				importpath = "github.com/ClickHouse/clickhouse-go/v2",
+				sum = "h1:Nbl/NZwoM6LGJm7smNBgvtdr/rxjlIssSW3eG/Nmb9E=",
+				version = "v2.0.12",
+			)`,
+			want: `go_deps = use_extension("//:extensions.bzl", "go_deps")
+
+			go_deps.gazelle_override(
+				build_extra_args = ["-go_naming_convention_external=go_default_library"],
+				directives = [
+					"gazelle:resolve go github.com/ClickHouse/clickhouse-go/v2/external @com_github_clickhouse_clickhouse_go_v2//external",
+					"gazelle:proto disable",
+				],
+				path = "github.com/ClickHouse/clickhouse-go/v2",
+			)`,
+		},
+		{
+			name: "archive overrides",
+			give: `go_repository(
+				name = "org_golang_x_tools_cmd_goimports",
+				build_extra_args = [
+					"-go_prefix=golang.org/x/tools",
+					"-exclude=**/testdata",
+				],
+				build_file_generation = "on",
+				build_file_proto_mode = "disable",
+				importpath = "golang.org/x/tools/cmd/goimports",
+				patch_args = ["-p1"],
+				strip_prefix = "golang.org/x/tools@v0.0.0-20200512131952-2bc93b1c0c88",
+				sha256 = "4a6497e0bf1f19c8089dd02e7ba1351ba787f434d62971ff14fb627e57914939",
+				patches = [
+					"//patches:org_golang_x_tools_cmd_goimports.patch",
+				],
+				urls = [
+					"https://goproxy.uberinternal.com/golang.org/x/tools/@v/v0.0.0-20200512131952-2bc93b1c0c88.zip",
+				],
+			)`,
+			want: `go_deps = use_extension("//:extensions.bzl", "go_deps")
+
+			go_deps.archive_override(
+				patch_strip = 1,
+				patches = [
+					"//patches:org_golang_x_tools_cmd_goimports.patch",
+				],
+				path = "golang.org/x/tools/cmd/goimports",
+				sha256 = "4a6497e0bf1f19c8089dd02e7ba1351ba787f434d62971ff14fb627e57914939",
+				strip_prefix = "golang.org/x/tools@v0.0.0-20200512131952-2bc93b1c0c88",
+				urls = [
+					"https://goproxy.uberinternal.com/golang.org/x/tools/@v/v0.0.0-20200512131952-2bc93b1c0c88.zip",
+				],
+			)
+
+			go_deps.gazelle_override(
+				build_extra_args = [
+					"-go_prefix=golang.org/x/tools",
+					"-exclude=**/testdata",
+				],
+				build_file_generation = "on",
+				directives = ["gazelle:proto disable"],
+				path = "golang.org/x/tools/cmd/goimports",
+			)`,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			w := t.TempDir()
+			testWorkspace := filepath.Join(w, "WORKSPACE")
+			if err := os.WriteFile(testWorkspace, []byte(removeTabsAndTrimLines(tt.give)), 0644); err != nil {
+				t.Errorf("error writing test workspace file: %v", err)
+			}
+
+			args := &mainArgs{
+				workspace:                  testWorkspace,
+				outputFile:                 filepath.Join(w, "output.bzl"),
+				defaultBuildFileGeneration: "on",
+				defaultBuildFileProtoMode:  "disable",
 			}
 
 			if err := run(*args, io.Discard); err != nil {