diff --git a/pkg/apis/certmanager/v1/types.go b/pkg/apis/certmanager/v1/types.go
index 9e8b6902521..31e737c60fa 100644
--- a/pkg/apis/certmanager/v1/types.go
+++ b/pkg/apis/certmanager/v1/types.go
@@ -146,10 +146,9 @@ const (
 	// set to either the configured value or the empty string.
 	IngressClassAnnotationKey = "kubernetes.io/ingress.class"
 
-	// IngressSecretTemplateAnnotations specifies arbitrary annotations on the Ingress resource to be set in the
-	// generated Certificate resource's secretTemplate. Existing annotations with the same key are overridden.
-	// The value is a regex that must fully match the annotation key.
-	IngressSecretTemplateAnnotations = "cert-manager.io/secret-template-annotations"
+	// IngressSecretTemplate can be used to set the secretTemplate field in the generated Certificate.
+	// The value is a JSON representation of secretTemplate and must not have any unknown fields.
+	IngressSecretTemplate = "cert-manager.io/secret-template"
 )
 
 // Annotation names for CertificateRequests
diff --git a/pkg/controller/certificate-shim/helper.go b/pkg/controller/certificate-shim/helper.go
index eab05db7dd0..ce6f59152e0 100644
--- a/pkg/controller/certificate-shim/helper.go
+++ b/pkg/controller/certificate-shim/helper.go
@@ -17,10 +17,10 @@ limitations under the License.
 package shimhelper
 
 import (
+	"encoding/json"
 	"errors"
 	"fmt"
 	"reflect"
-	"regexp"
 	"strconv"
 	"strings"
 	"time"
@@ -269,25 +269,22 @@ func translateAnnotations(crt *cmapi.Certificate, ingLikeAnnotations map[string]
 		}
 	}
 
-	if customAnnotationsRegexString, found := ingLikeAnnotations[cmapi.IngressSecretTemplateAnnotations]; found {
-		customAnnotationsRegex, err := regexp.Compile(customAnnotationsRegexString)
-		if err != nil {
-			return fmt.Errorf("%w %q: error parsing regexp: %q", errInvalidIngressAnnotation, cmapi.IngressSecretTemplateAnnotations, customAnnotationsRegexString)
+	if secretTemplateJson, found := ingLikeAnnotations[cmapi.IngressSecretTemplate]; found {
+		decoder := json.NewDecoder(strings.NewReader(secretTemplateJson))
+		decoder.DisallowUnknownFields()
+
+		var secretTemplate = new(cmapi.CertificateSecretTemplate)
+		if err := decoder.Decode(secretTemplate); err != nil {
+			return fmt.Errorf("%w %q: error parsing secret template JSON: %v", errInvalidIngressAnnotation, cmapi.IngressSecretTemplate, err)
 		}
-		for annotationKey, annotationValue := range ingLikeAnnotations {
-			match := customAnnotationsRegex.FindString(annotationKey)
-			if len(match) == len(annotationKey) {
-				if strings.HasPrefix(annotationKey, "cert-manager.io/") {
-					return fmt.Errorf("%w %q: regex must not match cert-manager.io/ annotations: %q", errInvalidIngressAnnotation, cmapi.IngressSecretTemplateAnnotations, customAnnotationsRegexString)
-				}
-				if crt.Spec.SecretTemplate == nil {
-					crt.Spec.SecretTemplate = &cmapi.CertificateSecretTemplate{
-						Annotations: map[string]string{},
-					}
-				}
-				crt.Spec.SecretTemplate.Annotations[annotationKey] = annotationValue
+		for annotationKey := range secretTemplate.Annotations {
+			if strings.HasPrefix(annotationKey, "cert-manager.io/") {
+				return fmt.Errorf("%w %q: secretTemplate must not have cert-manager.io/ annotations: %q", errInvalidIngressAnnotation, cmapi.IngressSecretTemplate, annotationKey)
 			}
 		}
+		if len(secretTemplate.Annotations) > 0 || len(secretTemplate.Labels) > 0 {
+			crt.Spec.SecretTemplate = secretTemplate
+		}
 	}
 
 	return nil
diff --git a/pkg/controller/certificate-shim/sync_test.go b/pkg/controller/certificate-shim/sync_test.go
index 2f39d5c7a50..bd98f36267c 100644
--- a/pkg/controller/certificate-shim/sync_test.go
+++ b/pkg/controller/certificate-shim/sync_test.go
@@ -544,12 +544,8 @@ func TestSync(t *testing.T) {
 					Name:      "ingress-name",
 					Namespace: gen.DefaultTestNamespace,
 					Annotations: map[string]string{
-						cmapi.IngressClusterIssuerNameAnnotationKey:          "issuer-name",
-						cmapi.IngressSecretTemplateAnnotations:               "secret-reflector.com.*",
-						"secret-replicator.com/ignored-annotation":           "ignored-value",
-						"www.secret-reflector.com/ignored-annotation":        "ignored-value",
-						"secret-reflector.com/reflection-enabled":            "true",
-						"secret-reflector.com/reflection-enabled-namespaces": "example-namespace",
+						cmapi.IngressClusterIssuerNameAnnotationKey: "issuer-name",
+						cmapi.IngressSecretTemplate:                 `{ "annotations": { "example-annotation" : "dummy-value" }, "labels": { "example-label" : "dummy-value" } }`,
 					},
 					UID: types.UID("ingress-name"),
 				},
@@ -576,8 +572,10 @@ func TestSync(t *testing.T) {
 						SecretName: "example-com-tls",
 						SecretTemplate: &cmapi.CertificateSecretTemplate{
 							Annotations: map[string]string{
-								"secret-reflector.com/reflection-enabled":            "true",
-								"secret-reflector.com/reflection-enabled-namespaces": "example-namespace",
+								"example-annotation": "dummy-value",
+							},
+							Labels: map[string]string{
+								"example-label": "dummy-value",
 							},
 						},
 						IssuerRef: cmmeta.ObjectReference{
@@ -590,7 +588,7 @@ func TestSync(t *testing.T) {
 			},
 		},
 		{
-			Name:   "secret template annotation should not match cert-manager.io/ annotations",
+			Name:   "secret template annotation should not allow cert-manager.io/ annotations",
 			Issuer: acmeClusterIssuer,
 			IngressLike: &networkingv1.Ingress{
 				ObjectMeta: metav1.ObjectMeta{
@@ -598,7 +596,7 @@ func TestSync(t *testing.T) {
 					Namespace: gen.DefaultTestNamespace,
 					Annotations: map[string]string{
 						cmapi.IngressClusterIssuerNameAnnotationKey: "issuer-name",
-						cmapi.IngressSecretTemplateAnnotations:      ".*cert-manager.io/.*",
+						cmapi.IngressSecretTemplate:                 `{ "annotations": { "cert-manager.io/disallowed-annotation" : "dummy-value" } }`,
 					},
 					UID: types.UID("ingress-name"),
 				},
@@ -614,7 +612,7 @@ func TestSync(t *testing.T) {
 			Err: true,
 		},
 		{
-			Name:   "secret template annotation should have valid regex",
+			Name:   "secret template annotation should not allow unknown fields",
 			Issuer: acmeClusterIssuer,
 			IngressLike: &networkingv1.Ingress{
 				ObjectMeta: metav1.ObjectMeta{
@@ -622,7 +620,7 @@ func TestSync(t *testing.T) {
 					Namespace: gen.DefaultTestNamespace,
 					Annotations: map[string]string{
 						cmapi.IngressClusterIssuerNameAnnotationKey: "issuer-name",
-						cmapi.IngressSecretTemplateAnnotations:      ")invalid] [regex(",
+						cmapi.IngressSecretTemplate:                 `{ "unknown-field": "true" }`,
 					},
 					UID: types.UID("ingress-name"),
 				},