diff --git a/mlir/lib/CAPI/CMakeLists.txt b/mlir/lib/CAPI/CMakeLists.txt
--- a/mlir/lib/CAPI/CMakeLists.txt
+++ b/mlir/lib/CAPI/CMakeLists.txt
@@ -10,12 +10,16 @@
 add_subdirectory(Debug)
 add_subdirectory(Dialect)
 add_subdirectory(Conversion)
-add_subdirectory(ExecutionEngine)
 add_subdirectory(Interfaces)
 add_subdirectory(IR)
 add_subdirectory(Registration)
 add_subdirectory(Transforms)
 
+# Only enable the ExecutionEngine if the native target is configured in.
+if(TARGET ${LLVM_NATIVE_ARCH})
+  add_subdirectory(ExecutionEngine)
+endif()
+
 # Build the optional CAPI dylib.
 if(MLIR_BUILD_MLIR_C_DYLIB)
   message(STATUS "Building MLIR-C dylib")
@@ -33,3 +37,4 @@
     endif()
   endif()
 endif()
+
diff --git a/mlir/lib/CMakeLists.txt b/mlir/lib/CMakeLists.txt
--- a/mlir/lib/CMakeLists.txt
+++ b/mlir/lib/CMakeLists.txt
@@ -4,7 +4,6 @@
 add_subdirectory(Analysis)
 add_subdirectory(Conversion)
 add_subdirectory(Dialect)
-add_subdirectory(ExecutionEngine)
 add_subdirectory(IR)
 add_subdirectory(Interfaces)
 add_subdirectory(Parser)
@@ -17,3 +16,8 @@
 add_subdirectory(Tools)
 add_subdirectory(Transforms)
 add_subdirectory(Translation)
+
+# Only enable the ExecutionEngine if the native target is configured in.
+if(TARGET ${LLVM_NATIVE_ARCH})
+  add_subdirectory(ExecutionEngine)
+endif()
\ No newline at end of file
diff --git a/mlir/python/CMakeLists.txt b/mlir/python/CMakeLists.txt
--- a/mlir/python/CMakeLists.txt
+++ b/mlir/python/CMakeLists.txt
@@ -292,17 +292,20 @@
   MLIRCAPIConversion
 )
 
-declare_mlir_python_extension(MLIRPythonExtension.ExecutionEngine
-  MODULE_NAME _mlirExecutionEngine
-  ADD_TO_PARENT MLIRPythonSources.ExecutionEngine
-  ROOT_DIR "${PYTHON_SOURCE_DIR}"
-  SOURCES
-    ExecutionEngineModule.cpp
-  PRIVATE_LINK_LIBS
-    LLVMSupport
-  EMBED_CAPI_LINK_LIBS
-    MLIRCAPIExecutionEngine
-)
+# Only enable the ExecutionEngine if the native target is configured in.
+if(TARGET ${LLVM_NATIVE_ARCH})
+  declare_mlir_python_extension(MLIRPythonExtension.ExecutionEngine
+    MODULE_NAME _mlirExecutionEngine
+    ADD_TO_PARENT MLIRPythonSources.ExecutionEngine
+    ROOT_DIR "${PYTHON_SOURCE_DIR}"
+    SOURCES
+      ExecutionEngineModule.cpp
+    PRIVATE_LINK_LIBS
+      LLVMSupport
+    EMBED_CAPI_LINK_LIBS
+      MLIRCAPIExecutionEngine
+  )
+endif()
 
 declare_mlir_python_extension(MLIRPythonExtension.GPUDialectPasses
   MODULE_NAME _mlirGPUPasses
diff --git a/mlir/test/CAPI/CMakeLists.txt b/mlir/test/CAPI/CMakeLists.txt
--- a/mlir/test/CAPI/CMakeLists.txt
+++ b/mlir/test/CAPI/CMakeLists.txt
@@ -19,13 +19,16 @@
   endif()
 endfunction(_add_capi_test_executable)
 
-_add_capi_test_executable(mlir-capi-execution-engine-test
-  execution_engine.c
-LINK_LIBS PRIVATE
-  MLIRCAPIConversion
-  MLIRCAPIExecutionEngine
-  MLIRCAPIRegistration
-)
+# Only enable the ExecutionEngine if the native target is configured in.
+if(TARGET ${LLVM_NATIVE_ARCH})
+  _add_capi_test_executable(mlir-capi-execution-engine-test
+    execution_engine.c
+  LINK_LIBS PRIVATE
+    MLIRCAPIConversion
+    MLIRCAPIExecutionEngine
+    MLIRCAPIRegistration
+  )
+endif()
 
 _add_capi_test_executable(mlir-capi-ir-test
   ir.c
diff --git a/mlir/test/CMakeLists.txt b/mlir/test/CMakeLists.txt
--- a/mlir/test/CMakeLists.txt
+++ b/mlir/test/CMakeLists.txt
@@ -75,7 +75,6 @@
 
 set(MLIR_TEST_DEPENDS
   FileCheck count not split-file
-  mlir-capi-execution-engine-test
   mlir-capi-ir-test
   mlir-capi-llvm-test
   mlir-capi-pass-test
@@ -89,9 +88,6 @@
   mlir-reduce
   mlir-tblgen
   mlir-translate
-  mlir_runner_utils
-  mlir_c_runner_utils
-  mlir_async_runtime
   )
 
 # The native target may not be enabled, in this case we won't
@@ -101,6 +97,10 @@
   list(APPEND MLIR_TEST_DEPENDS
     mlir-cpu-runner
     llc
+    mlir_async_runtime
+    mlir-capi-execution-engine-test
+    mlir_c_runner_utils
+    mlir_runner_utils
   )
 endif()