diff --git a/cmd/controller-gen/main.go b/cmd/controller-gen/main.go
index f880b04ce..b421028a9 100644
--- a/cmd/controller-gen/main.go
+++ b/cmd/controller-gen/main.go
@@ -24,6 +24,7 @@ import (
 	"strings"
 
 	"github.com/spf13/cobra"
+	"golang.org/x/tools/go/packages"
 
 	"sigs.k8s.io/controller-tools/pkg/applyconfiguration"
 	"sigs.k8s.io/controller-tools/pkg/crd"
@@ -129,6 +130,7 @@ func main() {
 	helpLevel := 0
 	whichLevel := 0
 	showVersion := false
+	var buildTags []string
 
 	cmd := &cobra.Command{
 		Use:   "controller-gen",
@@ -173,7 +175,8 @@ func main() {
 			}
 
 			// otherwise, set up the runtime for actually running the generators
-			rt, err := genall.FromOptions(optionsRegistry, rawOpts)
+			tagsFlag := fmt.Sprintf("-tags=%s", strings.Join(buildTags, ","))
+			rt, err := genall.FromOptionsWithConfig(&packages.Config{BuildFlags: []string{tagsFlag}}, optionsRegistry, rawOpts)
 			if err != nil {
 				return err
 			}
@@ -192,6 +195,7 @@ func main() {
 	cmd.Flags().CountVarP(&whichLevel, "which-markers", "w", "print out all markers available with the requested generators\n(up to -www for the most detailed output, or -wwww for json output)")
 	cmd.Flags().CountVarP(&helpLevel, "detailed-help", "h", "print out more detailed help\n(up to -hhh for the most detailed output, or -hhhh for json output)")
 	cmd.Flags().BoolVar(&showVersion, "version", false, "show version")
+	cmd.Flags().StringSliceVar(&buildTags, "load-build-tags", []string{"ignore_autogenerated"}, "build tags to use when loading Go packages")
 	cmd.Flags().Bool("help", false, "print out usage and a summary of options")
 	oldUsage := cmd.UsageFunc()
 	cmd.SetUsageFunc(func(c *cobra.Command) error {
diff --git a/pkg/genall/genall.go b/pkg/genall/genall.go
index 33f1f8c2f..b6f37409b 100644
--- a/pkg/genall/genall.go
+++ b/pkg/genall/genall.go
@@ -218,7 +218,11 @@ func (g GenerationContext) ReadFile(path string) ([]byte, error) {
 // ForRoots produces a Runtime to run the given generators against the
 // given packages.  It outputs to /dev/null by default.
 func (g Generators) ForRoots(rootPaths ...string) (*Runtime, error) {
-	roots, err := loader.LoadRoots(rootPaths...)
+	return g.ForRootsWithConfig(&packages.Config{}, rootPaths...)
+}
+
+func (g Generators) ForRootsWithConfig(cfg *packages.Config, rootPaths ...string) (*Runtime, error) {
+	roots, err := loader.LoadRootsWithConfig(cfg, rootPaths...)
 	if err != nil {
 		return nil, err
 	}
diff --git a/pkg/genall/options.go b/pkg/genall/options.go
index ac57d7bed..192235b76 100644
--- a/pkg/genall/options.go
+++ b/pkg/genall/options.go
@@ -20,6 +20,7 @@ import (
 	"fmt"
 	"strings"
 
+	"golang.org/x/tools/go/packages"
 	"sigs.k8s.io/controller-tools/pkg/markers"
 )
 
@@ -74,13 +75,17 @@ func RegistryFromOptions(optionsRegistry *markers.Registry, options []string) (*
 // further modified.  Not default generators are used if none are specified -- you can check
 // the output and rerun for that.
 func FromOptions(optionsRegistry *markers.Registry, options []string) (*Runtime, error) {
+	return FromOptionsWithConfig(&packages.Config{}, optionsRegistry, options)
+}
+
+func FromOptionsWithConfig(cfg *packages.Config, optionsRegistry *markers.Registry, options []string) (*Runtime, error) {
 	protoRt, err := protoFromOptions(optionsRegistry, options)
 	if err != nil {
 		return nil, err
 	}
 
 	// make the runtime
-	genRuntime, err := protoRt.Generators.ForRoots(protoRt.Paths...)
+	genRuntime, err := protoRt.Generators.ForRootsWithConfig(cfg, protoRt.Paths...)
 	if err != nil {
 		return nil, err
 	}
diff --git a/pkg/loader/loader.go b/pkg/loader/loader.go
index 2c5cf4c97..8062b72d8 100644
--- a/pkg/loader/loader.go
+++ b/pkg/loader/loader.go
@@ -374,8 +374,14 @@ func LoadRootsWithConfig(cfg *packages.Config, roots ...string) ([]*Package, err
 	if l.cfg.Fset == nil {
 		l.cfg.Fset = token.NewFileSet()
 	}
-	// put our build flags first so that callers can override them
-	l.cfg.BuildFlags = append([]string{"-tags", "ignore_autogenerated"}, l.cfg.BuildFlags...)
+
+	// put our build flags first so that callers can override them.
+	//
+	// NOTE: if callers provide their own `-tags` flag, then our hardcoded `ignore_autogenerated` tag
+	//   will be ignored. Callers that provide custom tags MUST include `ignore_autogenerated` in their
+	//   custom tag set if they want that tag to remain active. Users can explicitly pass custom build
+	//   flags with `-tags=""` to disable use of the default `ignore_autogenerated` tag.
+	l.cfg.BuildFlags = append([]string{"-tags=ignore_autogenerated"}, l.cfg.BuildFlags...)
 
 	// Visit the import graphs of the loaded, root packages. If an imported
 	// package refers to another loaded, root package, then replace the