diff --git a/src/app/app.cmake b/src/app/app.cmake
index d5e5ab1a..0a93b98b 100644
--- a/src/app/app.cmake
+++ b/src/app/app.cmake
@@ -203,7 +203,13 @@ target_link_libraries(yaze PRIVATE
 )
 if(YAZE_WITH_GRPC AND YAZE_PROTOBUF_TARGETS)
   target_link_libraries(yaze PRIVATE ${YAZE_PROTOBUF_TARGETS})
-  # NOTE: Removed /WHOLEARCHIVE - already linked transitively from libraries
+  # Apply /WHOLEARCHIVE only at executable level to avoid duplicate version.res
+  # This ensures protobuf internal symbols are included while preventing resource duplication
+  if(MSVC AND YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+    foreach(_yaze_proto_target IN LISTS YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+      target_link_options(yaze PRIVATE /WHOLEARCHIVE:$<TARGET_FILE:${_yaze_proto_target}>)
+    endforeach()
+  endif()
 endif()
 
 # Link test support library (yaze_editor needs TestManager)
diff --git a/src/app/emu/emu.cmake b/src/app/emu/emu.cmake
index c66fe9f9..ca6656da 100644
--- a/src/app/emu/emu.cmake
+++ b/src/app/emu/emu.cmake
@@ -34,6 +34,13 @@ if(YAZE_BUILD_EMU AND NOT YAZE_MINIMAL_BUILD)
     message(WARNING "yaze_emu needs yaze_test_support but TARGET not found")
   endif()
 
+  # Apply /WHOLEARCHIVE for protobuf at executable level (Windows)
+  if(WIN32 AND MSVC AND YAZE_WITH_GRPC AND YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+    foreach(_yaze_proto_target IN LISTS YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+      target_link_options(yaze_emu PRIVATE /WHOLEARCHIVE:$<TARGET_FILE:${_yaze_proto_target}>)
+    endforeach()
+  endif()
+
   # Test engine is always available when tests are built
   # No need for conditional definitions
 
@@ -53,6 +60,14 @@ if(YAZE_BUILD_EMU AND NOT YAZE_MINIMAL_BUILD)
     absl::strings
     absl::str_format
   )
+  
+  # Apply /WHOLEARCHIVE for protobuf at executable level (Windows)
+  if(WIN32 AND MSVC AND YAZE_WITH_GRPC AND YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+    foreach(_yaze_proto_target IN LISTS YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+      target_link_options(yaze_emu_test PRIVATE /WHOLEARCHIVE:$<TARGET_FILE:${_yaze_proto_target}>)
+    endforeach()
+  endif()
+  
   message(STATUS "✓ yaze_emu_test: Headless emulator test harness configured")
   message(STATUS "✓ yaze_emu: Standalone emulator executable configured")
 else()
diff --git a/src/cli/z3ed.cmake b/src/cli/z3ed.cmake
index 752a9add..631cd812 100644
--- a/src/cli/z3ed.cmake
+++ b/src/cli/z3ed.cmake
@@ -42,6 +42,12 @@ if(YAZE_WITH_GRPC)
   target_link_libraries(z3ed PRIVATE grpc++ grpc++_reflection)
   if(YAZE_PROTOBUF_TARGETS)
     target_link_libraries(z3ed PRIVATE ${YAZE_PROTOBUF_TARGETS})
-    # NOTE: Removed /WHOLEARCHIVE for protobuf - causes duplicate version.res in dependency chain
+    # Apply /WHOLEARCHIVE only at executable level to avoid duplicate version.res
+    # This ensures protobuf internal symbols are included while preventing resource duplication
+    if(MSVC AND YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+      foreach(_yaze_proto_target IN LISTS YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+        target_link_options(z3ed PRIVATE /WHOLEARCHIVE:$<TARGET_FILE:${_yaze_proto_target}>)
+      endforeach()
+    endif()
   endif()
 endif()
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index f3dc94a8..510ca402 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -47,8 +47,12 @@ if(YAZE_BUILD_TESTS)
       message(STATUS "Configuring Windows stack size for ${suite_name} to 16MB")
       if(MSVC)
         target_link_options(${suite_name} PRIVATE /STACK:16777216)
-        # NOTE: Removed /WHOLEARCHIVE for protobuf - causes LNK1241 duplicate version.res
-        # Protobuf symbols are already linked transitively from yaze_test_support
+        # Apply /WHOLEARCHIVE only at executable level to prevent duplicate version.res
+        if(YAZE_WITH_GRPC AND YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+          foreach(_yaze_proto_target IN LISTS YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+            target_link_options(${suite_name} PRIVATE /WHOLEARCHIVE:$<TARGET_FILE:${_yaze_proto_target}>)
+          endforeach()
+        endif()
       else()
         target_link_options(${suite_name} PRIVATE -Wl,--stack,16777216)
       endif()
diff --git a/tools/test_helpers/CMakeLists.txt b/tools/test_helpers/CMakeLists.txt
index 6c40884b..9531cd40 100644
--- a/tools/test_helpers/CMakeLists.txt
+++ b/tools/test_helpers/CMakeLists.txt
@@ -50,6 +50,12 @@ foreach(TOOL ${HELPER_TOOLS})
   if(WIN32)
     if(MSVC)
       target_link_options(${TOOL} PRIVATE /STACK:16777216)
+      # Apply /WHOLEARCHIVE for protobuf at executable level
+      if(YAZE_WITH_GRPC AND YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+        foreach(_yaze_proto_target IN LISTS YAZE_PROTOBUF_WHOLEARCHIVE_TARGETS)
+          target_link_options(${TOOL} PRIVATE /WHOLEARCHIVE:$<TARGET_FILE:${_yaze_proto_target}>)
+        endforeach()
+      endif()
     elseif(MINGW OR CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
       target_link_options(${TOOL} PRIVATE -Wl,--stack,16777216)
     else()