diff --git a/cmd/acmesolver/main.go b/cmd/acmesolver/main.go
index 9d38da5df..36f3bd803 100644
--- a/cmd/acmesolver/main.go
+++ b/cmd/acmesolver/main.go
@@ -17,9 +17,6 @@ limitations under the License.
 package main
 
 import (
-	"fmt"
-	"os"
-
 	"github.com/cert-manager/cert-manager/acmesolver-binary/app"
 	"github.com/cert-manager/cert-manager/internal/cmd/util"
 	logf "github.com/cert-manager/cert-manager/pkg/logs"
@@ -39,7 +36,7 @@ func main() {
 	cmd := app.NewACMESolverCommand(stopCh)
 
 	if err := cmd.Execute(); err != nil {
-		fmt.Fprintf(os.Stderr, "%s\n", err)
+		logf.Log.Error(err, "error executing command")
 		util.SetExitCode(err)
 	}
 }
diff --git a/cmd/cainjector/main.go b/cmd/cainjector/main.go
index fcca310d7..0568e182e 100644
--- a/cmd/cainjector/main.go
+++ b/cmd/cainjector/main.go
@@ -39,11 +39,10 @@ func main() {
 	ctrl.SetLogger(logf.Log)
 
 	ctx := util.ContextWithStopCh(context.Background(), stopCh)
-
 	cmd := app.NewCommandStartInjectorController(ctx, os.Stdout, os.Stderr)
 
 	if err := cmd.Execute(); err != nil {
-		cmd.PrintErrln(err)
+		logf.Log.Error(err, "error executing command")
 		util.SetExitCode(err)
 	}
 }
diff --git a/cmd/controller/main.go b/cmd/controller/main.go
index 0086c7cea..bf454d6b1 100644
--- a/cmd/controller/main.go
+++ b/cmd/controller/main.go
@@ -32,7 +32,7 @@ func main() {
 	cmd := app.NewCommandStartCertManagerController(stopCh)
 
 	if err := cmd.Execute(); err != nil {
-		logf.Log.Error(err, "error while executing")
+		logf.Log.Error(err, "error executing command")
 		util.SetExitCode(err)
 	}
 }
diff --git a/pkg/acme/webhook/cmd/cmd.go b/pkg/acme/webhook/cmd/cmd.go
index d290de98f..6c8de15df 100644
--- a/pkg/acme/webhook/cmd/cmd.go
+++ b/pkg/acme/webhook/cmd/cmd.go
@@ -17,7 +17,6 @@ limitations under the License.
 package cmd
 
 import (
-	"flag"
 	"os"
 	"runtime"
 
@@ -46,7 +45,7 @@ func RunWebhookServer(groupName string, hooks ...webhook.Solver) {
 	}
 
 	cmd := server.NewCommandStartWebhookServer(os.Stdout, os.Stderr, stopCh, groupName, hooks...)
-	cmd.Flags().AddGoFlagSet(flag.CommandLine)
+
 	if err := cmd.Execute(); err != nil {
 		logf.Log.Error(err, "error executing command")
 		util.SetExitCode(err)
diff --git a/pkg/acme/webhook/cmd/server/start.go b/pkg/acme/webhook/cmd/server/start.go
index 400070216..66995774e 100644
--- a/pkg/acme/webhook/cmd/server/start.go
+++ b/pkg/acme/webhook/cmd/server/start.go
@@ -25,15 +25,19 @@ import (
 
 	genericapiserver "k8s.io/apiserver/pkg/server"
 	genericoptions "k8s.io/apiserver/pkg/server/options"
+	"k8s.io/component-base/logs"
 
 	"github.com/cert-manager/cert-manager/pkg/acme/webhook"
 	whapi "github.com/cert-manager/cert-manager/pkg/acme/webhook/apis/acme/v1alpha1"
 	"github.com/cert-manager/cert-manager/pkg/acme/webhook/apiserver"
+	logf "github.com/cert-manager/cert-manager/pkg/logs"
 )
 
 const defaultEtcdPathPrefix = "/registry/acme.cert-manager.io"
 
 type WebhookServerOptions struct {
+	Logging *logs.Options
+
 	RecommendedOptions *genericoptions.RecommendedOptions
 
 	SolverGroup string
@@ -45,6 +49,8 @@ type WebhookServerOptions struct {
 
 func NewWebhookServerOptions(out, errOut io.Writer, groupName string, solvers ...webhook.Solver) *WebhookServerOptions {
 	o := &WebhookServerOptions{
+		Logging: logs.NewOptions(),
+
 		// TODO we will nil out the etcd storage options.  This requires a later level of k8s.io/apiserver
 		RecommendedOptions: genericoptions.NewRecommendedOptions(
 			defaultEtcdPathPrefix,
@@ -84,12 +90,17 @@ func NewCommandStartWebhookServer(out, errOut io.Writer, stopCh <-chan struct{},
 	}
 
 	flags := cmd.Flags()
+	logf.AddFlags(o.Logging, flags)
 	o.RecommendedOptions.AddFlags(flags)
 
 	return cmd
 }
 
 func (o WebhookServerOptions) Validate(args []string) error {
+	if err := logf.ValidateAndApply(o.Logging); err != nil {
+		return err
+	}
+
 	return nil
 }
 
diff --git a/pkg/logs/logs.go b/pkg/logs/logs.go
index 62c662a51..c79fe96c6 100644
--- a/pkg/logs/logs.go
+++ b/pkg/logs/logs.go
@@ -82,7 +82,6 @@ func AddFlags(opts *logs.Options, fs *pflag.FlagSet) {
 			}
 		})
 	}
-	_ = fs.Set("logtostderr", "true")
 
 	{
 		var allFlags pflag.FlagSet