diff --git a/.chloggen/featuregates-into-cli-go.yaml b/.chloggen/featuregates-into-cli-go.yaml
new file mode 100755
index 0000000000..0e39a4b37f
--- /dev/null
+++ b/.chloggen/featuregates-into-cli-go.yaml
@@ -0,0 +1,16 @@
+# One of 'breaking', 'deprecation', 'new_component', 'enhancement', 'bug_fix'
+change_type: 'breaking'
+
+# The name of the component, or a single word describing the area of concern, (e.g. collector, target allocator, auto-instrumentation, opamp, github action)
+component: 'operator'
+
+# A brief description of the change. Surround your text with quotes ("") if it needs to start with a backtick (`).
+note: remove featuregate `operator.autoinstrumentation.go`. Use command line flag `--enable-go-instrumentation` instead
+
+# One or more tracking issues related to the change
+issues: [2675]
+
+# (Optional) One or more lines of additional information to render under the primary note.
+# These lines will be padded with 2 spaces and then inserted directly into the document.
+# Use pipe (|) for multiline entries.
+subtext:
diff --git a/.github/workflows/e2e.yaml b/.github/workflows/e2e.yaml
index 7ee5c89d79..b09eafa381 100644
--- a/.github/workflows/e2e.yaml
+++ b/.github/workflows/e2e.yaml
@@ -34,6 +34,8 @@ jobs:
          - e2e-multi-instrumentation
          - e2e-metadata-filters
        include:
+         - group: e2e-instrumentation
+           setup: "add-operator-arg OPERATOR_ARG=--enable-go-instrumentation prepare-e2e"
          - group: e2e-multi-instrumentation
            setup: "add-operator-arg OPERATOR_ARG=--enable-multi-instrumentation prepare-e2e"
          - group: e2e-metadata-filters
diff --git a/internal/config/main.go b/internal/config/main.go
index 03b00d2dbd..c3149b258b 100644
--- a/internal/config/main.go
+++ b/internal/config/main.go
@@ -47,6 +47,7 @@ type Config struct {
 	enableMultiInstrumentation          bool
 	enableApacheHttpdInstrumentation    bool
 	enableDotNetInstrumentation         bool
+	enableGoInstrumentation             bool
 	enableNginxInstrumentation          bool
 	enablePythonInstrumentation         bool
 	enableJavaInstrumentation           bool
@@ -89,6 +90,7 @@ func New(opts ...Option) Config {
 		enableMultiInstrumentation:          o.enableMultiInstrumentation,
 		enableApacheHttpdInstrumentation:    o.enableApacheHttpdInstrumentation,
 		enableDotNetInstrumentation:         o.enableDotNetInstrumentation,
+		enableGoInstrumentation:             o.enableGoInstrumentation,
 		enableNginxInstrumentation:          o.enableNginxInstrumentation,
 		enablePythonInstrumentation:         o.enablePythonInstrumentation,
 		enableJavaInstrumentation:           o.enableJavaInstrumentation,
@@ -149,6 +151,11 @@ func (c *Config) EnableDotNetAutoInstrumentation() bool {
 	return c.enableDotNetInstrumentation
 }
 
+// EnableGoAutoInstrumentation is true when the operator supports Go auto instrumentation.
+func (c *Config) EnableGoAutoInstrumentation() bool {
+	return c.enableGoInstrumentation
+}
+
 // EnableNginxAutoInstrumentation is true when the operator supports nginx auto instrumentation.
 func (c *Config) EnableNginxAutoInstrumentation() bool {
 	return c.enableNginxInstrumentation
diff --git a/internal/config/options.go b/internal/config/options.go
index 961cd8df65..daf5d69067 100644
--- a/internal/config/options.go
+++ b/internal/config/options.go
@@ -46,6 +46,7 @@ type options struct {
 	enableMultiInstrumentation          bool
 	enableApacheHttpdInstrumentation    bool
 	enableDotNetInstrumentation         bool
+	enableGoInstrumentation             bool
 	enableNginxInstrumentation          bool
 	enablePythonInstrumentation         bool
 	enableJavaInstrumentation           bool
@@ -104,6 +105,11 @@ func WithEnableDotNetInstrumentation(s bool) Option {
 		o.enableDotNetInstrumentation = s
 	}
 }
+func WithEnableGoInstrumentation(s bool) Option {
+	return func(o *options) {
+		o.enableGoInstrumentation = s
+	}
+}
 func WithEnableNginxInstrumentation(s bool) Option {
 	return func(o *options) {
 		o.enableNginxInstrumentation = s
diff --git a/main.go b/main.go
index 0d89d09b22..83bc6ef1a2 100644
--- a/main.go
+++ b/main.go
@@ -112,6 +112,7 @@ func main() {
 		enableMultiInstrumentation       bool
 		enableApacheHttpdInstrumentation bool
 		enableDotNetInstrumentation      bool
+		enableGoInstrumentation          bool
 		enablePythonInstrumentation      bool
 		enableNginxInstrumentation       bool
 		enableJavaInstrumentation        bool
@@ -141,6 +142,7 @@ func main() {
 	pflag.BoolVar(&enableMultiInstrumentation, "enable-multi-instrumentation", false, "Controls whether the operator supports multi instrumentation")
 	pflag.BoolVar(&enableApacheHttpdInstrumentation, constants.FlagApacheHttpd, true, "Controls whether the operator supports Apache HTTPD auto-instrumentation")
 	pflag.BoolVar(&enableDotNetInstrumentation, constants.FlagDotNet, true, "Controls whether the operator supports dotnet auto-instrumentation")
+	pflag.BoolVar(&enableGoInstrumentation, constants.FlagGo, false, "Controls whether the operator supports Go auto-instrumentation")
 	pflag.BoolVar(&enablePythonInstrumentation, constants.FlagPython, true, "Controls whether the operator supports python auto-instrumentation")
 	pflag.BoolVar(&enableNginxInstrumentation, constants.FlagNginx, false, "Controls whether the operator supports nginx auto-instrumentation")
 	pflag.BoolVar(&enableJavaInstrumentation, constants.FlagJava, true, "Controls whether the operator supports java auto-instrumentation")
@@ -186,6 +188,7 @@ func main() {
 		"enable-multi-instrumentation", enableMultiInstrumentation,
 		"enable-apache-httpd-instrumentation", enableApacheHttpdInstrumentation,
 		"enable-dotnet-instrumentation", enableDotNetInstrumentation,
+		"enable-go-instrumentation", enableGoInstrumentation,
 		"enable-python-instrumentation", enablePythonInstrumentation,
 		"enable-nginx-instrumentation", enableNginxInstrumentation,
 		"enable-java-instrumentation", enableJavaInstrumentation,
@@ -208,6 +211,7 @@ func main() {
 		config.WithEnableMultiInstrumentation(enableMultiInstrumentation),
 		config.WithEnableApacheHttpdInstrumentation(enableApacheHttpdInstrumentation),
 		config.WithEnableDotNetInstrumentation(enableDotNetInstrumentation),
+		config.WithEnableGoInstrumentation(enableGoInstrumentation),
 		config.WithEnableNginxInstrumentation(enableNginxInstrumentation),
 		config.WithEnablePythonInstrumentation(enablePythonInstrumentation),
 		config.WithEnableJavaInstrumentation(enableJavaInstrumentation),
diff --git a/pkg/constants/env.go b/pkg/constants/env.go
index 76442a1846..fb15aa6ca4 100644
--- a/pkg/constants/env.go
+++ b/pkg/constants/env.go
@@ -39,6 +39,7 @@ const (
 
 	FlagApacheHttpd = "enable-apache-httpd-instrumentation"
 	FlagDotNet      = "enable-dotnet-instrumentation"
+	FlagGo          = "enable-go-instrumentation"
 	FlagPython      = "enable-python-instrumentation"
 	FlagNginx       = "enable-nginx-instrumentation"
 	FlagJava        = "enable-java-instrumentation"
diff --git a/pkg/featuregate/featuregate.go b/pkg/featuregate/featuregate.go
index 9ff966a4f9..2e2798cc85 100644
--- a/pkg/featuregate/featuregate.go
+++ b/pkg/featuregate/featuregate.go
@@ -31,6 +31,12 @@ var (
 		featuregate.WithRegisterDescription("controls whether the operator supports NodeJS auto-instrumentation"),
 		featuregate.WithRegisterFromVersion("v0.76.1"),
 	)
+	EnableNginxAutoInstrumentationSupport = featuregate.GlobalRegistry().MustRegister(
+		"operator.autoinstrumentation.nginx",
+		featuregate.StageAlpha,
+		featuregate.WithRegisterDescription("controls whether the operator supports Nginx auto-instrumentation"),
+		featuregate.WithRegisterFromVersion("v0.86.0"),
+	)
 	EnableGoAutoInstrumentationSupport = featuregate.GlobalRegistry().MustRegister(
 		"operator.autoinstrumentation.go",
 		featuregate.StageAlpha,
diff --git a/pkg/instrumentation/podmutator.go b/pkg/instrumentation/podmutator.go
index b22bdad6dd..d82564cde3 100644
--- a/pkg/instrumentation/podmutator.go
+++ b/pkg/instrumentation/podmutator.go
@@ -278,7 +278,7 @@ func (pm *instPodMutator) Mutate(ctx context.Context, ns corev1.Namespace, pod c
 		logger.Error(err, "failed to select an OpenTelemetry Instrumentation instance for this pod")
 		return pod, err
 	}
-	if featuregate.EnableGoAutoInstrumentationSupport.IsEnabled() || inst == nil {
+	if pm.config.EnableGoAutoInstrumentation() || inst == nil {
 		insts.Go.Instrumentation = inst
 	} else {
 		logger.Error(err, "support for Go auto instrumentation is not enabled")
diff --git a/pkg/instrumentation/podmutator_test.go b/pkg/instrumentation/podmutator_test.go
index d786e63c31..ffc69463a8 100644
--- a/pkg/instrumentation/podmutator_test.go
+++ b/pkg/instrumentation/podmutator_test.go
@@ -2721,16 +2721,7 @@ func TestMutatePod(t *testing.T) {
 					},
 				},
 			},
-			config: config.New(config.WithEnableMultiInstrumentation(true)),
-			setFeatureGates: func(t *testing.T) {
-				originalVal := featuregate.EnableGoAutoInstrumentationSupport.IsEnabled()
-
-				require.NoError(t, colfeaturegate.GlobalRegistry().Set(featuregate.EnableGoAutoInstrumentationSupport.ID(), true))
-				t.Cleanup(func() {
-					require.NoError(t, colfeaturegate.GlobalRegistry().Set(featuregate.EnableGoAutoInstrumentationSupport.ID(), originalVal))
-
-				})
-			},
+			config: config.New(config.WithEnableGoInstrumentation(true)),
 		},
 		{
 			name: "go injection feature gate disabled",
@@ -2811,6 +2802,7 @@ func TestMutatePod(t *testing.T) {
 					},
 				},
 			},
+			config: config.New(config.WithEnableGoInstrumentation(false)),
 		},
 		{
 			name: "apache httpd injection, true",
diff --git a/pkg/instrumentation/upgrade/upgrade.go b/pkg/instrumentation/upgrade/upgrade.go
index 469c566440..aeedf119e6 100644
--- a/pkg/instrumentation/upgrade/upgrade.go
+++ b/pkg/instrumentation/upgrade/upgrade.go
@@ -33,7 +33,6 @@ import (
 var (
 	defaultAnnotationToGate = map[string]*featuregate2.Gate{
 		constants.AnnotationDefaultAutoInstrumentationNodeJS: featuregate.EnableNodeJSAutoInstrumentationSupport,
-		constants.AnnotationDefaultAutoInstrumentationGo:     featuregate.EnableGoAutoInstrumentationSupport,
 	}
 )
 
@@ -60,6 +59,7 @@ func NewInstrumentationUpgrade(client client.Client, logger logr.Logger, recorde
 	defaultAnnotationToConfig := map[string]autoInstConfig{
 		constants.AnnotationDefaultAutoInstrumentationApacheHttpd: {constants.FlagApacheHttpd, cfg.EnableApacheHttpdAutoInstrumentation()},
 		constants.AnnotationDefaultAutoInstrumentationDotNet:      {constants.FlagDotNet, cfg.EnableDotNetAutoInstrumentation()},
+		constants.AnnotationDefaultAutoInstrumentationGo:          {constants.FlagGo, cfg.EnableGoAutoInstrumentation()},
 		constants.AnnotationDefaultAutoInstrumentationNginx:       {constants.FlagNginx, cfg.EnableNginxAutoInstrumentation()},
 		constants.AnnotationDefaultAutoInstrumentationPython:      {constants.FlagPython, cfg.EnablePythonAutoInstrumentation()},
 		constants.AnnotationDefaultAutoInstrumentationJava:        {constants.FlagJava, cfg.EnableJavaAutoInstrumentation()},
@@ -132,6 +132,11 @@ func (u *InstrumentationUpgrade) upgrade(_ context.Context, inst v1alpha1.Instru
 						upgraded.Spec.DotNet.Image = u.DefaultAutoInstDotNet
 						upgraded.Annotations[annotation] = u.DefaultAutoInstDotNet
 					}
+				case constants.AnnotationDefaultAutoInstrumentationGo:
+					if inst.Spec.Go.Image == autoInst {
+						upgraded.Spec.Go.Image = u.DefaultAutoInstGo
+						upgraded.Annotations[annotation] = u.DefaultAutoInstGo
+					}
 				case constants.AnnotationDefaultAutoInstrumentationNginx:
 					if inst.Spec.Nginx.Image == autoInst {
 						upgraded.Spec.Nginx.Image = u.DefaultAutoInstNginx
diff --git a/pkg/instrumentation/upgrade/upgrade_test.go b/pkg/instrumentation/upgrade/upgrade_test.go
index 9bb39f3893..bc52a4d3a4 100644
--- a/pkg/instrumentation/upgrade/upgrade_test.go
+++ b/pkg/instrumentation/upgrade/upgrade_test.go
@@ -22,7 +22,6 @@ import (
 	"github.com/go-logr/logr"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	colfeaturegate "go.opentelemetry.io/collector/featuregate"
 	corev1 "k8s.io/api/core/v1"
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"k8s.io/apimachinery/pkg/types"
@@ -32,16 +31,9 @@ import (
 	"github.com/open-telemetry/opentelemetry-operator/apis/v1alpha1"
 	"github.com/open-telemetry/opentelemetry-operator/internal/config"
 	"github.com/open-telemetry/opentelemetry-operator/pkg/constants"
-	"github.com/open-telemetry/opentelemetry-operator/pkg/featuregate"
 )
 
 func TestUpgrade(t *testing.T) {
-	originalVal := featuregate.EnableGoAutoInstrumentationSupport.IsEnabled()
-	require.NoError(t, colfeaturegate.GlobalRegistry().Set(featuregate.EnableGoAutoInstrumentationSupport.ID(), true))
-	t.Cleanup(func() {
-		require.NoError(t, colfeaturegate.GlobalRegistry().Set(featuregate.EnableGoAutoInstrumentationSupport.ID(), originalVal))
-	})
-
 	nsName := strings.ToLower(t.Name())
 	err := k8sClient.Create(context.Background(), &corev1.Namespace{
 		ObjectMeta: metav1.ObjectMeta{
@@ -74,6 +66,7 @@ func TestUpgrade(t *testing.T) {
 			config.WithAutoInstrumentationNginxImage("nginx:1"),
 			config.WithEnableApacheHttpdInstrumentation(true),
 			config.WithEnableDotNetInstrumentation(true),
+			config.WithEnableGoInstrumentation(true),
 			config.WithEnableNginxInstrumentation(true),
 			config.WithEnablePythonInstrumentation(true),
 			config.WithEnableJavaInstrumentation(true),
@@ -100,6 +93,7 @@ func TestUpgrade(t *testing.T) {
 		config.WithAutoInstrumentationNginxImage("nginx:2"),
 		config.WithEnableApacheHttpdInstrumentation(true),
 		config.WithEnableDotNetInstrumentation(true),
+		config.WithEnableGoInstrumentation(true),
 		config.WithEnableNginxInstrumentation(true),
 		config.WithEnablePythonInstrumentation(true),
 		config.WithEnableJavaInstrumentation(true),