diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index bd7114bd03..a26cb89536 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -843,12 +843,16 @@ if (WIN32)
     if (MSVC)
       foreach(type EXE STATIC SHARED)
         if (NOT type MATCHES STATIC)
-          set(CMAKE_${type}_LINKER_FLAGS_RELEASE "${CMAKE_${type}_LINKER_FLAGS_RELEASE} /OPT:REF,ICF,LBR")
-          set(CMAKE_${type}_LINKER_FLAGS_RELEASE "${CMAKE_${type}_LINKER_FLAGS_RELEASE} /INCREMENTAL:NO")
-          set(CMAKE_${type}_LINKER_FLAGS_RELWITHDEBINFO "${CMAKE_${type}_LINKER_FLAGS_RELWITHDEBINFO} /OPT:REF,ICF,LBR")
-          set(CMAKE_${type}_LINKER_FLAGS_RELWITHDEBINFO "${CMAKE_${type}_LINKER_FLAGS_RELWITHDEBINFO} /INCREMENTAL:NO")
-          set(CMAKE_${type}_LINKER_FLAGS_MINSIZEREL "${CMAKE_${type}_LINKER_FLAGS_MINSIZEREL} /OPT:REF,ICF,LBR")
-          set(CMAKE_${type}_LINKER_FLAGS_MINSIZEREL "${CMAKE_${type}_LINKER_FLAGS_MINSIZEREL} /INCREMENTAL:NO")
+          # The WinML internal toolchain does not allow link's "additional options" to contain optimization
+          # flags (/OPT#); these are already specified using msbuild properties.
+          if (NOT DEFINED onnxruntime_DISABLE_LINKER_OPT_FLAGS)
+            set(CMAKE_${type}_LINKER_FLAGS_RELEASE "${CMAKE_${type}_LINKER_FLAGS_RELEASE} /OPT:REF,ICF,LBR")
+            set(CMAKE_${type}_LINKER_FLAGS_RELEASE "${CMAKE_${type}_LINKER_FLAGS_RELEASE} /INCREMENTAL:NO")
+            set(CMAKE_${type}_LINKER_FLAGS_RELWITHDEBINFO "${CMAKE_${type}_LINKER_FLAGS_RELWITHDEBINFO} /OPT:REF,ICF,LBR")
+            set(CMAKE_${type}_LINKER_FLAGS_RELWITHDEBINFO "${CMAKE_${type}_LINKER_FLAGS_RELWITHDEBINFO} /INCREMENTAL:NO")
+            set(CMAKE_${type}_LINKER_FLAGS_MINSIZEREL "${CMAKE_${type}_LINKER_FLAGS_MINSIZEREL} /OPT:REF,ICF,LBR")
+            set(CMAKE_${type}_LINKER_FLAGS_MINSIZEREL "${CMAKE_${type}_LINKER_FLAGS_MINSIZEREL} /INCREMENTAL:NO")
+          endif()
         endif()
         if (onnxruntime_ENABLE_LTO AND NOT onnxruntime_USE_CUDA)
           set(CMAKE_${type}_LINKER_FLAGS_RELEASE "${CMAKE_${type}_LINKER_FLAGS_RELEASE} /LTCG")