diff --git a/Source/cmCacheManager.cxx b/Source/cmCacheManager.cxx
index 864df8e05..ed09545cb 100644
--- a/Source/cmCacheManager.cxx
+++ b/Source/cmCacheManager.cxx
@@ -750,6 +750,10 @@ void cmCacheManager::AddCacheEntry(const char* key,
     }
   e.SetProperty("HELPSTRING", helpString? helpString :
                 "(This variable does not exist and should not be used)");
+  if (this->Cache[key].Value == e.Value)
+    {
+    this->CMakeInstance->UnwatchUnusedCli(key);
+    }
   this->Cache[key] = e;
 }
 
diff --git a/Source/cmake.cxx b/Source/cmake.cxx
index ae62edb9f..e757f3a6e 100644
--- a/Source/cmake.cxx
+++ b/Source/cmake.cxx
@@ -383,11 +383,22 @@ bool cmake::SetCacheArgs(const std::vector<std::string>& args)
       cmCacheManager::CacheEntryType type = cmCacheManager::UNINITIALIZED;
       if(cmCacheManager::ParseEntry(entry.c_str(), var, value, type))
         {
+        // The value is transformed if it is a filepath for example, so
+        // we can't compare whether the value is already in the cache until
+        // after we call AddCacheEntry.
+        const char *cachedValue =
+                              this->CacheManager->GetCacheValue(var.c_str());
+
         this->CacheManager->AddCacheEntry(var.c_str(), value.c_str(),
           "No help, variable specified on the command line.", type);
         if(this->WarnUnusedCli)
           {
-          this->WatchUnusedCli(var.c_str());
+          if (!cachedValue
+              || strcmp(this->CacheManager->GetCacheValue(var.c_str()),
+                        cachedValue) != 0)
+            {
+            this->WatchUnusedCli(var.c_str());
+            }
           }
         }
       else
diff --git a/Tests/CMakeLists.txt b/Tests/CMakeLists.txt
index 0b221e885..a91eac7cc 100644
--- a/Tests/CMakeLists.txt
+++ b/Tests/CMakeLists.txt
@@ -1618,17 +1618,23 @@ ${CMake_BINARY_DIR}/bin/cmake -DVERSION=master -P ${CMake_SOURCE_DIR}/Utilities/
     FAIL_REGULAR_EXPRESSION "CMake Warning .*VariableUnusedViaUnset.CMakeLists.txt:5 \\(set\\):")
   list(APPEND TEST_BUILD_DIRS "${CMake_BINARY_DIR}/Tests/WarnUnusedUnusedViaUnset")
 
-  add_test(WarnUnusedCliUnused ${CMAKE_CTEST_COMMAND}
-    --build-and-test
-    "${CMake_SOURCE_DIR}/Tests/VariableUsage"
-    "${CMake_BINARY_DIR}/Tests/WarnUnusedCliUnused"
-    ${build_generator_args}
-    --build-noclean
-    --build-project WarnUnusedCliUnused
-    --build-options "-DUNUSED_CLI_VARIABLE=Unused")
-  set_tests_properties(WarnUnusedCliUnused PROPERTIES
-    PASS_REGULAR_EXPRESSION "CMake Warning:.*Manually-specified variables were not used by the project:.*  UNUSED_CLI_VARIABLE")
-  list(APPEND TEST_BUILD_DIRS "${CMake_BINARY_DIR}/Tests/WarnUnusedCliUnused")
+  if("${CMAKE_TEST_GENERATOR}" MATCHES "Makefile")
+    # Ninja does not support ADDITIONAL_MAKE_CLEAN_FILES and therefore fails
+    # this test. (See #13371)
+    # Apparently Visual Studio does not support it either. As the MakeClean
+    # test above is only run with the Makefiles generator, only run this
+    # test with the Makefiles generator also.
+    add_test(WarnUnusedCliUnused ${CMAKE_CTEST_COMMAND}
+      --build-and-test
+      "${CMake_SOURCE_DIR}/Tests/WarnUnusedCliUnused"
+      "${CMake_BINARY_DIR}/Tests/WarnUnusedCliUnused"
+      ${build_generator_args}
+      --build-project WarnUnusedCliUnused
+      --build-options "-DUNUSED_CLI_VARIABLE=Unused")
+    set_tests_properties(WarnUnusedCliUnused PROPERTIES
+      PASS_REGULAR_EXPRESSION "CMake Warning:.*Manually-specified variables were not used by the project:.*  UNUSED_CLI_VARIABLE")
+    list(APPEND TEST_BUILD_DIRS "${CMake_BINARY_DIR}/Tests/WarnUnusedCliUnused")
+  endif()
 
   add_test(WarnUnusedCliUsed ${CMAKE_CTEST_COMMAND}
     --build-and-test
diff --git a/Tests/WarnUnusedCliUnused/CMakeLists.txt b/Tests/WarnUnusedCliUnused/CMakeLists.txt
new file mode 100644
index 000000000..7ed69bf3c
--- /dev/null
+++ b/Tests/WarnUnusedCliUnused/CMakeLists.txt
@@ -0,0 +1,9 @@
+cmake_minimum_required(VERSION 2.8)
+
+project(WarnUnusedCliUnused)
+
+set_directory_properties(PROPERTIES
+  ADDITIONAL_MAKE_CLEAN_FILES "${CMAKE_BINARY_DIR}/CMakeCache.txt"
+)
+
+add_library(dummy empty.cpp)
diff --git a/Tests/WarnUnusedCliUnused/empty.cpp b/Tests/WarnUnusedCliUnused/empty.cpp
new file mode 100644
index 000000000..7279c5e0b
--- /dev/null
+++ b/Tests/WarnUnusedCliUnused/empty.cpp
@@ -0,0 +1,7 @@
+#ifdef _WIN32
+__declspec(dllexport)
+#endif
+int empty(void)
+{
+  return 0;
+}