diff --git a/.chloggen/fix-labels-annotations-filter.yaml b/.chloggen/fix-labels-annotations-filter.yaml
new file mode 100755
index 0000000000..bde0808c84
--- /dev/null
+++ b/.chloggen/fix-labels-annotations-filter.yaml
@@ -0,0 +1,16 @@
+# One of 'breaking', 'deprecation', 'new_component', 'enhancement', 'bug_fix'
+change_type: 'bug_fix'
+
+# 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: collector
+
+# A brief description of the change. Surround your text with quotes ("") if it needs to start with a backtick (`).
+note: Fix of Labels and Annotations filter
+
+# One or more tracking issues related to the change
+issues: [2770]
+
+# (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 9bd466986f..ea6a3d7ead 100644
--- a/.github/workflows/e2e.yaml
+++ b/.github/workflows/e2e.yaml
@@ -40,7 +40,7 @@ jobs:
          - group: e2e-multi-instrumentation
            setup: "add-multi-instrumentation-params prepare-e2e"
          - group: e2e-metadata-filters
-           setup: "add-operator-arg OPERATOR_ARG='--annotations-filter=*filter.out --labels=*filter.out' prepare-e2e"
+           setup: "add-operator-arg OPERATOR_ARG='--annotations-filter=.*filter.out --labels=.*filter.out' prepare-e2e"
          - group: e2e-automatic-rbac
            setup: "add-rbac-permissions-to-operator prepare-e2e"
     steps:
diff --git a/internal/manifests/manifestutils/labels.go b/internal/manifests/manifestutils/labels.go
index e70c018b22..3605e38c12 100644
--- a/internal/manifests/manifestutils/labels.go
+++ b/internal/manifests/manifestutils/labels.go
@@ -25,8 +25,9 @@ import (
 )
 
 func IsFilteredSet(sourceSet string, filterSet []string) bool {
-	for _, pattern := range filterSet {
-		if match, _ := regexp.MatchString(pattern, sourceSet); match {
+	for _, basePattern := range filterSet {
+		pattern, _ := regexp.Compile(basePattern)
+		if match := pattern.MatchString(sourceSet); match {
 			return match
 		}
 	}
diff --git a/main.go b/main.go
index dbf9be361f..fb856fd123 100644
--- a/main.go
+++ b/main.go
@@ -20,6 +20,7 @@ import (
 	"flag"
 	"fmt"
 	"os"
+	"regexp"
 	"runtime"
 	"strings"
 	"time"
@@ -158,9 +159,8 @@ func main() {
 	stringFlagOrEnv(&autoInstrumentationGo, "auto-instrumentation-go-image", "RELATED_IMAGE_AUTO_INSTRUMENTATION_GO", fmt.Sprintf("ghcr.io/open-telemetry/opentelemetry-go-instrumentation/autoinstrumentation-go:%s", v.AutoInstrumentationGo), "The default OpenTelemetry Go instrumentation image. This image is used when no image is specified in the CustomResource.")
 	stringFlagOrEnv(&autoInstrumentationApacheHttpd, "auto-instrumentation-apache-httpd-image", "RELATED_IMAGE_AUTO_INSTRUMENTATION_APACHE_HTTPD", fmt.Sprintf("ghcr.io/open-telemetry/opentelemetry-operator/autoinstrumentation-apache-httpd:%s", v.AutoInstrumentationApacheHttpd), "The default OpenTelemetry Apache HTTPD instrumentation image. This image is used when no image is specified in the CustomResource.")
 	stringFlagOrEnv(&autoInstrumentationNginx, "auto-instrumentation-nginx-image", "RELATED_IMAGE_AUTO_INSTRUMENTATION_NGINX", fmt.Sprintf("ghcr.io/open-telemetry/opentelemetry-operator/autoinstrumentation-apache-httpd:%s", v.AutoInstrumentationNginx), "The default OpenTelemetry Nginx instrumentation image. This image is used when no image is specified in the CustomResource.")
-	pflag.StringArrayVar(&labelsFilter, "label", []string{}, "Labels to filter away from propagating onto deploys")
-	pflag.StringArrayVar(&annotationsFilter, "annotations-filter", []string{}, "Annotations to filter away from propagating onto deploys. It should be a string array containing patterns, which are literal strings optionally containing a * wildcard character. Example: --annotations-filter=*filter.out will filter out annotations that looks like: annotation.filter.out: true")
-	pflag.IntVar(&webhookPort, "webhook-port", 9443, "The port the webhook endpoint binds to.")
+	pflag.StringArrayVar(&labelsFilter, "label", []string{}, "Labels to filter away from propagating onto deploys. It should be a string array containing patterns, which are literal strings optionally containing a * wildcard character. Example: --labels-filter=.*filter.out will filter out labels that looks like: label.filter.out: true")
+	pflag.StringArrayVar(&annotationsFilter, "annotations-filter", []string{}, "Annotations to filter away from propagating onto deploys. It should be a string array containing patterns, which are literal strings optionally containing a * wildcard character. Example: --annotations-filter=.*filter.out will filter out annotations that looks like: annotation.filter.out: true")
 	pflag.StringVar(&tlsOpt.minVersion, "tls-min-version", "VersionTLS12", "Minimum TLS version supported. Value must match version names from https://golang.org/pkg/crypto/tls/#pkg-constants.")
 	pflag.StringSliceVar(&tlsOpt.cipherSuites, "tls-cipher-suites", nil, "Comma-separated list of cipher suites for the server. Values are from tls package constants (https://golang.org/pkg/crypto/tls/#pkg-constants). If omitted, the default Go cipher suites will be used")
 	pflag.Parse()
@@ -305,6 +305,23 @@ func main() {
 		setupLog.Info("Openshift CRDs are not installed, skipping adding to scheme.")
 	}
 
+	if cfg.AnnotationsFilter() != nil {
+		for _, basePattern := range cfg.AnnotationsFilter() {
+			_, compileErr := regexp.Compile(basePattern)
+			if compileErr != nil {
+				setupLog.Error(compileErr, "could not compile the regexp pattern for Annotations filter")
+			}
+		}
+	}
+	if cfg.LabelsFilter() != nil {
+		for _, basePattern := range cfg.LabelsFilter() {
+			_, compileErr := regexp.Compile(basePattern)
+			if compileErr != nil {
+				setupLog.Error(compileErr, "could not compile the regexp pattern for Labels filter")
+			}
+		}
+	}
+
 	err = addDependencies(ctx, mgr, cfg, v)
 	if err != nil {
 		setupLog.Error(err, "failed to add/run bootstrap dependencies to the controller manager")