diff --git a/cmd/cainjector/app/cainjector.go b/cmd/cainjector/app/cainjector.go
index ac96bc4ea..681fe7283 100644
--- a/cmd/cainjector/app/cainjector.go
+++ b/cmd/cainjector/app/cainjector.go
@@ -27,6 +27,7 @@ import (
 
 	"github.com/cert-manager/cert-manager/cainjector-binary/app/options"
 	config "github.com/cert-manager/cert-manager/internal/apis/config/cainjector"
+	"github.com/cert-manager/cert-manager/internal/apis/config/cainjector/validation"
 	cmdutil "github.com/cert-manager/cert-manager/internal/cmd/util"
 
 	cainjectorconfigfile "github.com/cert-manager/cert-manager/pkg/cainjector/configfile"
@@ -88,6 +89,10 @@ servers and webhook servers.`,
 				return err
 			}
 
+			if err := validation.ValidateCAInjectorConfiguration(cainjectorConfig); err != nil {
+				return fmt.Errorf("error validating flags: %w", err)
+			}
+
 			if err := logf.ValidateAndApplyAsField(&cainjectorConfig.Logging, field.NewPath("logging")); err != nil {
 				return fmt.Errorf("failed to validate cainjector logging flags: %w", err)
 			}
diff --git a/cmd/controller/app/start.go b/cmd/controller/app/start.go
index 05dcbcf81..aae4ca6f5 100644
--- a/cmd/controller/app/start.go
+++ b/cmd/controller/app/start.go
@@ -27,6 +27,7 @@ import (
 
 	"github.com/cert-manager/cert-manager/controller-binary/app/options"
 	config "github.com/cert-manager/cert-manager/internal/apis/config/controller"
+	"github.com/cert-manager/cert-manager/internal/apis/config/controller/validation"
 	cmdutil "github.com/cert-manager/cert-manager/internal/cmd/util"
 
 	_ "github.com/cert-manager/cert-manager/pkg/controller/acmechallenges"
@@ -99,6 +100,10 @@ to renew certificates at an appropriate time before expiry.`,
 				return err
 			}
 
+			if err := validation.ValidateControllerConfiguration(controllerConfig); err != nil {
+				return fmt.Errorf("error validating flags: %w", err)
+			}
+
 			if err := logf.ValidateAndApplyAsField(&controllerConfig.Logging, field.NewPath("logging")); err != nil {
 				return fmt.Errorf("failed to validate controller logging flags: %w", err)
 			}
diff --git a/cmd/webhook/app/webhook.go b/cmd/webhook/app/webhook.go
index 0c5fd470c..12fa8ef1b 100644
--- a/cmd/webhook/app/webhook.go
+++ b/cmd/webhook/app/webhook.go
@@ -26,6 +26,7 @@ import (
 	"k8s.io/apimachinery/pkg/util/validation/field"
 
 	config "github.com/cert-manager/cert-manager/internal/apis/config/webhook"
+	"github.com/cert-manager/cert-manager/internal/apis/config/webhook/validation"
 	cmdutil "github.com/cert-manager/cert-manager/internal/cmd/util"
 	cmwebhook "github.com/cert-manager/cert-manager/internal/webhook"
 	logf "github.com/cert-manager/cert-manager/pkg/logs"
@@ -94,6 +95,10 @@ functionality for cert-manager.`,
 				return err
 			}
 
+			if err := validation.ValidateWebhookConfiguration(webhookConfig); err != nil {
+				return fmt.Errorf("error validating flags: %w", err)
+			}
+
 			if err := logf.ValidateAndApplyAsField(&webhookConfig.Logging, field.NewPath("logging")); err != nil {
 				return fmt.Errorf("failed to validate webhook logging flags: %w", err)
 			}