diff --git a/java/com/google/gerrit/plugins/codeowners/api/CheckCodeOwnerConfigFilesInput.java b/java/com/google/gerrit/plugins/codeowners/api/CheckCodeOwnerConfigFilesInput.java
new file mode 100644
index 0000000..f06edf4
--- /dev/null
+++ b/java/com/google/gerrit/plugins/codeowners/api/CheckCodeOwnerConfigFilesInput.java
@@ -0,0 +1,29 @@
+// Copyright (C) 2020 The Android Open Source Project
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package com.google.gerrit.plugins.codeowners.api;
+
+/**
+ * The input for the {@link com.google.gerrit.plugins.codeowners.restapi.CheckCodeOwnerConfigFiles}
+ * REST endpoint.
+ */
+public class CheckCodeOwnerConfigFilesInput {
+  /**
+   * Whether code owner config files in branches for which the code owners functionality is disabled
+   * should be validated too.
+   *
+   * <p>By default unset, {@code false}.
+   */
+  public Boolean validateDisabledBranches;
+}
diff --git a/java/com/google/gerrit/plugins/codeowners/api/ProjectCodeOwners.java b/java/com/google/gerrit/plugins/codeowners/api/ProjectCodeOwners.java
index 4d3785b..b2823ea 100644
--- a/java/com/google/gerrit/plugins/codeowners/api/ProjectCodeOwners.java
+++ b/java/com/google/gerrit/plugins/codeowners/api/ProjectCodeOwners.java
@@ -33,6 +33,34 @@
 
   /** Request to check code owner config files. */
   abstract class CheckCodeOwnerConfigFilesRequest {
+    private boolean validateDisabledBranches;
+
+    /**
+     * Includes code owner config files in branches for which the code owners functionality is
+     * disabled into the validation.
+     */
+    public CheckCodeOwnerConfigFilesRequest validateDisabledBranches() {
+      return validateDisabledBranches(true);
+    }
+
+    /**
+     * Sets whether code owner config files in branches for which the code owners functionality is
+     * disabled should be validated.
+     */
+    public CheckCodeOwnerConfigFilesRequest validateDisabledBranches(
+        boolean validateDisabledBranches) {
+      this.validateDisabledBranches = validateDisabledBranches;
+      return this;
+    }
+
+    /**
+     * Whether code owner config files in branches for which the code owners functionality is
+     * disabled should be validated.
+     */
+    public boolean isValidateDisabledBranches() {
+      return validateDisabledBranches;
+    }
+
     /**
      * Executes the request to check the code owner config files and retrieves the result of the
      * validation.
diff --git a/java/com/google/gerrit/plugins/codeowners/api/ProjectCodeOwnersImpl.java b/java/com/google/gerrit/plugins/codeowners/api/ProjectCodeOwnersImpl.java
index 813f6a8..750d98d 100644
--- a/java/com/google/gerrit/plugins/codeowners/api/ProjectCodeOwnersImpl.java
+++ b/java/com/google/gerrit/plugins/codeowners/api/ProjectCodeOwnersImpl.java
@@ -17,7 +17,6 @@
 import static com.google.gerrit.server.api.ApiUtil.asRestApiException;
 
 import com.google.gerrit.extensions.api.config.ConsistencyCheckInfo.ConsistencyProblemInfo;
-import com.google.gerrit.extensions.common.Input;
 import com.google.gerrit.extensions.restapi.IdString;
 import com.google.gerrit.extensions.restapi.RestApiException;
 import com.google.gerrit.plugins.codeowners.restapi.CheckCodeOwnerConfigFiles;
@@ -83,7 +82,9 @@
       public Map<String, Map<String, List<ConsistencyProblemInfo>>> check()
           throws RestApiException {
         try {
-          return checkCodeOwnerConfigFiles.apply(projectResource, new Input()).value();
+          CheckCodeOwnerConfigFilesInput input = new CheckCodeOwnerConfigFilesInput();
+          input.validateDisabledBranches = isValidateDisabledBranches();
+          return checkCodeOwnerConfigFiles.apply(projectResource, input).value();
         } catch (Exception e) {
           throw asRestApiException("Cannot check code owner config files", e);
         }
diff --git a/java/com/google/gerrit/plugins/codeowners/restapi/CheckCodeOwnerConfigFiles.java b/java/com/google/gerrit/plugins/codeowners/restapi/CheckCodeOwnerConfigFiles.java
index 7dc9d62..cb55949 100644
--- a/java/com/google/gerrit/plugins/codeowners/restapi/CheckCodeOwnerConfigFiles.java
+++ b/java/com/google/gerrit/plugins/codeowners/restapi/CheckCodeOwnerConfigFiles.java
@@ -21,13 +21,14 @@
 import com.google.common.collect.LinkedListMultimap;
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.Multimaps;
+import com.google.common.flogger.FluentLogger;
 import com.google.gerrit.entities.BranchNameKey;
 import com.google.gerrit.extensions.api.config.ConsistencyCheckInfo.ConsistencyProblemInfo;
-import com.google.gerrit.extensions.common.Input;
 import com.google.gerrit.extensions.restapi.AuthException;
 import com.google.gerrit.extensions.restapi.Response;
 import com.google.gerrit.extensions.restapi.RestApiException;
 import com.google.gerrit.extensions.restapi.RestModifyView;
+import com.google.gerrit.plugins.codeowners.api.CheckCodeOwnerConfigFilesInput;
 import com.google.gerrit.plugins.codeowners.backend.CodeOwnerBackend;
 import com.google.gerrit.plugins.codeowners.backend.CodeOwnerConfig;
 import com.google.gerrit.plugins.codeowners.backend.CodeOwnerConfigScanner;
@@ -60,7 +61,10 @@
  * not be used in any critical path where performance matters.
  */
 @Singleton
-public class CheckCodeOwnerConfigFiles implements RestModifyView<ProjectResource, Input> {
+public class CheckCodeOwnerConfigFiles
+    implements RestModifyView<ProjectResource, CheckCodeOwnerConfigFilesInput> {
+  private static final FluentLogger logger = FluentLogger.forEnclosingClass();
+
   private final CurrentUser currentUser;
   private final PermissionBackend permissionBackend;
   private final Provider<ListBranches> listBranches;
@@ -86,7 +90,7 @@
 
   @Override
   public Response<Map<String, Map<String, List<ConsistencyProblemInfo>>>> apply(
-      ProjectResource projectResource, Input input)
+      ProjectResource projectResource, CheckCodeOwnerConfigFilesInput input)
       throws RestApiException, PermissionBackendException, IOException {
     if (!currentUser.isIdentifiedUser()) {
       throw new AuthException("Authentication required");
@@ -98,10 +102,17 @@
         .project(projectResource.getNameKey())
         .check(ProjectPermission.WRITE_CONFIG);
 
+    logger.atFine().log(
+        "checking code owner config files for project %s (validateDisabledBranches = %s)",
+        projectResource.getNameKey(), input.validateDisabledBranches);
+
     ImmutableMap.Builder<String, Map<String, List<ConsistencyProblemInfo>>> resultsByBranchBuilder =
         ImmutableMap.builder();
     branches(projectResource)
-        .filter(branchNameKey -> !codeOwnersPluginConfiguration.isDisabled(branchNameKey))
+        .filter(
+            branchNameKey ->
+                validateDisabledBranches(input)
+                    || !codeOwnersPluginConfiguration.isDisabled(branchNameKey))
         .forEach(
             branchNameKey ->
                 resultsByBranchBuilder.put(branchNameKey.branch(), checkBranch(branchNameKey)));
@@ -167,4 +178,8 @@
             "unknown message type %s for message %s",
             commitValidationMessage.getType(), commitValidationMessage.getMessage()));
   }
+
+  private static boolean validateDisabledBranches(CheckCodeOwnerConfigFilesInput input) {
+    return input.validateDisabledBranches != null && input.validateDisabledBranches;
+  }
 }
diff --git a/javatests/com/google/gerrit/plugins/codeowners/acceptance/api/CheckCodeOwnerConfigFilesIT.java b/javatests/com/google/gerrit/plugins/codeowners/acceptance/api/CheckCodeOwnerConfigFilesIT.java
index 47d78fa..f742ffe 100644
--- a/javatests/com/google/gerrit/plugins/codeowners/acceptance/api/CheckCodeOwnerConfigFilesIT.java
+++ b/javatests/com/google/gerrit/plugins/codeowners/acceptance/api/CheckCodeOwnerConfigFilesIT.java
@@ -85,6 +85,20 @@
   }
 
   @Test
+  @GerritConfig(name = "plugin.code-owners.disabledBranch", value = "refs/meta/config")
+  public void validateDisabledBranches() throws Exception {
+    assertThat(
+            projectCodeOwnersApiFactory
+                .project(project)
+                .checkCodeOwnerConfigFiles()
+                .validateDisabledBranches()
+                .check())
+        .containsExactly(
+            "refs/heads/master", ImmutableMap.of(),
+            "refs/meta/config", ImmutableMap.of());
+  }
+
+  @Test
   public void noIssuesInCodeOwnerConfigFile() throws Exception {
     // Create some code owner config files.
     codeOwnerConfigOperations
diff --git a/resources/Documentation/rest-api.md b/resources/Documentation/rest-api.md
index 242c362..5c23d5b 100644
--- a/resources/Documentation/rest-api.md
+++ b/resources/Documentation/rest-api.md
@@ -63,8 +63,13 @@
 
 Requires that the caller is an owner of the project.
 
+Input options can be set in the request body as a
+[CheckCodeOwnerConfigFilesInput](#check-code-owner-config-files-input) entity.
+
 No validation is done for branches for which the code owner functionality is
-[disabled](config.html#codeOwnersDisabledBranch).
+[disabled](config.html#codeOwnersDisabledBranch), unless
+`validate_disabled_branches` is set to `true` in the
+[input](#check-code-owner-config-files-input).
 
 As a response a map is returned that maps a branch name to a map that maps an
 owner configuration file path to a list of
@@ -370,6 +375,16 @@
 
 ---
 
+### <a id="check-code-owner-config-files-input"> CheckCodeOwnerConfigFilesInput
+The `CheckCodeOwnerConfigFilesInput` allows to set options for the [Check Code
+Owner Config Files REST endpoint](#check-code-owner-config-files).
+
+| Field Name                   |          | Description |
+| ---------------------------- | -------- | ----------- |
+| `validate_disabled_branches` | optional | Whether code owner config files in branches for which the code owners functionality is disabled should be validated too. By default unset, `false`.
+
+---
+
 ### <a id="code-owner-config-info"> CodeOwnerConfigInfo
 The `CodeOwnerConfigInfo` entity contains information about a code owner config
 for a path.