diff --git a/CMakeLists.txt b/CMakeLists.txt
index ec782239..f163b64d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -216,7 +216,7 @@ set(FlatBuffers_GRPCTest_SRCS
 # source_group(Compiler FILES ${FlatBuffers_Compiler_SRCS})
 # source_group(Tests FILES ${FlatBuffers_Tests_SRCS})
 
-if(EXISTS "${CMAKE_TOOLCHAIN_FILE}")
+if(EXISTS "${CMAKE_TOOLCHAIN_FILE}" AND NOT DEFINED VCPKG_TOOLCHAIN)
   # do not apply any global settings if the toolchain
   # is being configured externally
   message(STATUS "Using toolchain file: ${CMAKE_TOOLCHAIN_FILE}.")