diff --git a/ets2panda/aot/main.cpp b/ets2panda/aot/main.cpp
index 420240cb0ee8c3f829f32ba08e3e68afa017d0f0..36daabba059094436418834d72a6bc1b9a95d88d 100644
--- a/ets2panda/aot/main.cpp
+++ b/ets2panda/aot/main.cpp
@@ -27,6 +27,7 @@
 #include "util/perfMetrics.h"
 #include "libpandabase/os/stacktrace.h"
 #include "generated/diagnostic.h"
+#include "generated/options.h"
 
 #include <iostream>
 #include <memory>
@@ -193,8 +194,7 @@ static int Run(Span<const char *const> args)
 
     es2panda::Compiler compiler(options->GetExtension(), options->GetThread(), std::move(pluginsOpt.value()));
     if (options->IsListPhases()) {
-        std::cerr << "Available phases:" << std::endl;
-        std::cerr << compiler.GetPhasesList();
+        std::cerr << "Available phases:" << std::endl << compiler.GetPhasesList();
         diagnosticEngine.FlushDiagnostic();
         return 1;
     }
@@ -213,6 +213,10 @@ static int Run(Span<const char *const> args)
             auto [buf, size] = options->CStrParserInputContents();
             parserInput = std::string_view(buf, size);
         }
+        if (options->WasSetArktsconfig() && !options->ArkTSConfig()->IsOutDirDefault() && options->GetOutputFlag()) {
+            diagnosticEngine.LogDiagnostic(diagnostic::REWRITE_OUTPUT_IN_CLI,
+                                           ark::es2panda::util::DiagnosticMessageParams());
+        }
         es2panda::SourceFile input(sourceFile, parserInput, options->IsModule(), options->GetOutput());
         res = CompileFromSource(compiler, input, *options.get(), diagnosticEngine);
     }
diff --git a/ets2panda/util/arktsconfig.cpp b/ets2panda/util/arktsconfig.cpp
index c63bc91f971c9a515734b64896780acb05cab800..b670f2dfd65a6b00bd21229ba33de9a16e5b15be 100644
--- a/ets2panda/util/arktsconfig.cpp
+++ b/ets2panda/util/arktsconfig.cpp
@@ -368,6 +368,9 @@ bool ArkTsConfig::ParseCompilerOptions(std::string &arktsConfigDir, const JsonOb
     // Parse "baseUrl", "outDir", "rootDir", "cacheDir"
     baseUrl_ = MakeAbsolute(ValueOrEmptyString(compilerOptions, BASE_URL), arktsConfigDir);
     outDir_ = MakeAbsolute(ValueOrEmptyString(compilerOptions, OUT_DIR), arktsConfigDir);
+    if (ValueOrEmptyString(compilerOptions, OUT_DIR) == "") {
+        isOutDirDefault_ = true;
+    }
     rootDir_ = ValueOrEmptyString(compilerOptions, ROOT_DIR);
     if (!rootDir_.empty() &&
         !Check(ark::os::file::File::IsDirectory(rootDir_), diagnostic::NOT_A_DIR, {"rootDir " + rootDir_})) {
diff --git a/ets2panda/util/arktsconfig.h b/ets2panda/util/arktsconfig.h
index eeb613ccb2c4339009805288befbdc7d23141a6d..5a9616b28fb8eb1891eccc63cd9b4afec0657953 100644
--- a/ets2panda/util/arktsconfig.h
+++ b/ets2panda/util/arktsconfig.h
@@ -134,6 +134,10 @@ public:
 
     void ResolveAllDependenciesInArkTsConfig();
 
+    bool IsOutDirDefault() const
+    {
+        return isOutDirDefault_;
+    }
     const std::string &ConfigPath() const
     {
         return configPath_;
@@ -219,6 +223,8 @@ private:
                          std::map<std::string, ExternalModuleData, CompareByLength> &dependenciesMap);
 
     bool isParsed_ = false;
+    bool isOutDirDefault_ = false;
+
     std::string configPath_;
 
     std::string package_ {};
diff --git a/ets2panda/util/diagnostic/warning.yaml b/ets2panda/util/diagnostic/warning.yaml
index 5d2579c02557ad6190fc322af03f9144d475dbd0..967ba6258c03d33476e114f56a80ed0a132955f3 100644
--- a/ets2panda/util/diagnostic/warning.yaml
+++ b/ets2panda/util/diagnostic/warning.yaml
@@ -105,6 +105,10 @@ warning:
   id: 6
   message: "Replace the lambda function with a regular function."
 
+- name: REWRITE_OUTPUT_IN_CLI
+  id: 31
+  message: "Output presented in config, used from cli args"
+
 - name: SETTER_LOOP
   id: 24
   message: "Assigning new value to the property inside its setter may lead to an endless loop."
diff --git a/ets2panda/util/options.cpp b/ets2panda/util/options.cpp
index dbb5e1fbee52249f632b57df0dd2b8e7f290e9fa..e5642b964d4f7b551a187ddbb63ca4521fea7a83 100644
--- a/ets2panda/util/options.cpp
+++ b/ets2panda/util/options.cpp
@@ -208,6 +208,9 @@ bool Options::Parse(Span<const char *const> args)
     if (!CallPandArgParser(es2pandaArgs)) {
         return false;
     }
+    if (WasSetOutput()) {
+        outputFlag_ = true;
+    }
 
     if (IsVersion()) {
         std::cerr << GetVersion();
diff --git a/ets2panda/util/options.h b/ets2panda/util/options.h
index 7b115a50f17c2c58da2552dda683c98b1d1d78f2..5b6b077c43c18f74f7ab75ed2365712ac4f29c49 100644
--- a/ets2panda/util/options.h
+++ b/ets2panda/util/options.h
@@ -170,6 +170,11 @@ public:
         return astVerifierEachPhase_ || astVerifierPhases_.find(std::string(phase)) != astVerifierPhases_.end();
     }
 
+    bool GetOutputFlag() const
+    {
+        return outputFlag_;
+    }
+
 private:
     template <typename T>
     static bool CallPandArgParser(const std::vector<std::string> &args, T &options,
@@ -204,6 +209,7 @@ private:
     Logger::Level logLevel_ {Logger::Level::ERROR};
     EvalMode evalMode_ = {EvalMode::NONE};
     util::DiagnosticEngine &diagnosticEngine_;
+    bool outputFlag_ = false;
 };
 }  // namespace ark::es2panda::util