diff --git a/src/mono/wasi/wasi.proj b/src/mono/wasi/wasi.proj
index d601f2c9e09ab6..611d7969f034b8 100644
--- a/src/mono/wasi/wasi.proj
+++ b/src/mono/wasi/wasi.proj
@@ -218,7 +218,6 @@
       <CMakeBuildRuntimeConfigureCmd>$(CMakeBuildRuntimeConfigureCmd) -DICU_LIB_DIR=&quot;$(ICULibDir.TrimEnd('\/'))&quot;</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd>$(CMakeBuildRuntimeConfigureCmd) -DMONO_ARTIFACTS_DIR=&quot;$(MonoArtifactsPath.TrimEnd('\/'))&quot;</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd>$(CMakeBuildRuntimeConfigureCmd) -DNATIVE_BIN_DIR=&quot;$(NativeBinDir.TrimEnd('\/'))&quot;</CMakeBuildRuntimeConfigureCmd>
-      <CMakeBuildRuntimeConfigureCmd Condition="'$(WasmEnableSIMD)' == 'true' and '$(Configuration)' == 'Release'">$(CMakeBuildRuntimeConfigureCmd) -DWASM_OPT_ADDITIONAL_FLAGS=&quot;--enable-simd&quot;</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd Condition="'$(MonoWasmThreads)' == 'true'">$(CMakeBuildRuntimeConfigureCmd) -DDISABLE_THREADS=0</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd Condition="'$(OS)' == 'Windows_NT'">call &quot;$(RepositoryEngineeringDir)native\init-vs-env.cmd&quot; wasm &amp;&amp; $(CMakeBuildRuntimeConfigureCmd)</CMakeBuildRuntimeConfigureCmd>
 
diff --git a/src/mono/wasm/Wasm.Build.Tests/WasmSIMDTests.cs b/src/mono/wasm/Wasm.Build.Tests/WasmSIMDTests.cs
index 96183d8cdeac74..de1a5683138ab8 100644
--- a/src/mono/wasm/Wasm.Build.Tests/WasmSIMDTests.cs
+++ b/src/mono/wasm/Wasm.Build.Tests/WasmSIMDTests.cs
@@ -24,7 +24,6 @@ public WasmSIMDTests(ITestOutputHelper output, SharedBuildPerTestClassFixture bu
 
         [Theory]
         [MemberData(nameof(MainMethodSimdTestData), parameters: new object[] { /*aot*/ false, RunHost.All, true /* simd */ })]
-        [MemberData(nameof(MainMethodSimdTestData), parameters: new object[] { /*aot*/ false, RunHost.All, false /* simd */ })]
         public void Build_NoAOT_ShouldNotRelink(BuildArgs buildArgs, RunHost host, string id)
         {
             string projectName = $"build_with_workload_no_aot";
diff --git a/src/mono/wasm/build/WasmApp.Native.targets b/src/mono/wasm/build/WasmApp.Native.targets
index 34736613dd8f6a..877c420b891482 100644
--- a/src/mono/wasm/build/WasmApp.Native.targets
+++ b/src/mono/wasm/build/WasmApp.Native.targets
@@ -24,6 +24,7 @@
       _SetWasmBuildNativeDefaults
     </_BeforeWasmBuildAppDependsOn>
 
+    <_EmccDefaultFlags Condition="'$(WasmEnableSIMD)' == 'true'">-msimd128</_EmccDefaultFlags>
     <_ExeExt Condition="$([MSBuild]::IsOSPlatform('WINDOWS'))">.exe</_ExeExt>
     <WasmUseEMSDK_PATH Condition="'$(WasmUseEMSDK_PATH)' == '' and '$(EMSDK_PATH)' != '' and Exists('$(MSBuildThisFileDirectory)WasmApp.InTree.targets')">true</WasmUseEMSDK_PATH>
   </PropertyGroup>
@@ -115,6 +116,12 @@
       <!-- removing legacy interop needs relink -->
       <WasmBuildNative Condition="'$(WasmBuildNative)' == '' and '$(WasmEnableLegacyJsInterop)' == 'false'" >true</WasmBuildNative>
 
+      <!-- disabling SIMD needs relink -->
+      <WasmBuildNative Condition="'$(WasmBuildNative)' == '' and '$(WasmEnableSIMD)' == 'false'" >true</WasmBuildNative>
+
+      <!-- disabling EH needs relink -->
+      <WasmBuildNative Condition="'$(WasmBuildNative)' == '' and '$(WasmEnableExceptionHandling)' == 'false'" >true</WasmBuildNative>
+
       <!-- InvariantTimezone and InvariantGlobalization need rebuild -->
       <WasmBuildNative Condition="'$(WasmBuildNative)' == '' and '$(InvariantTimezone)' == 'true'">true</WasmBuildNative>
       <WasmBuildNative Condition="'$(WasmBuildNative)' == '' and '$(InvariantGlobalization)' == 'true'">true</WasmBuildNative>
@@ -213,7 +220,6 @@
       <_EmccCommonFlags Include="-v"                                Condition="'$(EmccVerbose)' != 'false'" />
       <_EmccCommonFlags Include="-s DISABLE_EXCEPTION_CATCHING=0"   Condition="'$(WasmEnableExceptionHandling)' == 'false'" />
       <_EmccCommonFlags Include="-fwasm-exceptions"                 Condition="'$(WasmEnableExceptionHandling)' == 'true'" />
-      <_EmccCommonFlags Include="-msimd128"                         Condition="'$(WasmEnableSIMD)' == 'true' and '$(_WasmShouldAOT)' == 'true'" />
 
       <_EmccIncludePaths Include="$(_WasmIntermediateOutputPath.TrimEnd('\/'))" />
       <_EmccIncludePaths Include="$(_WasmRuntimePackIncludeDir)mono-2.0" />
@@ -345,7 +351,7 @@
     </ItemGroup>
     <EmccCompile
           SourceFiles="@(_WasmSourceFileToCompile)"
-          Arguments='"@$(_EmccDefaultFlagsRsp)" "@$(_EmccCompileRsp)"'
+          Arguments='"@$(_EmccDefaultFlagsRsp)" $(_EmccDefaultFlags) "@$(_EmccCompileRsp)"'
           EnvironmentVariables="@(EmscriptenEnvVars)"
           DisableParallelCompile="$(DisableParallelEmccCompile)"
           OutputMessageImportance="$(_EmccCompileOutputMessageImportance)">
@@ -367,7 +373,7 @@
     <Message Text="Compiling assembly bitcode files with $(EmccLinkOptimizationFlag) ..." Importance="High" Condition="@(_BitCodeFile->Count()) > 0" />
     <EmccCompile
           SourceFiles="@(_BitCodeFile)"
-          Arguments="&quot;@$(_EmccDefaultFlagsRsp)&quot; &quot;@$(_EmccCompileBitcodeRsp)&quot;"
+          Arguments="&quot;@$(_EmccDefaultFlagsRsp)&quot; $(_EmccDefaultFlags) &quot;@$(_EmccCompileBitcodeRsp)&quot;"
           EnvironmentVariables="@(EmscriptenEnvVars)"
           DisableParallelCompile="$(DisableParallelEmccCompile)"
           OutputMessageImportance="$(_EmccCompileOutputMessageImportance)">
@@ -483,7 +489,7 @@
     <Message Text="Linking for initial memory %24(EmccInitialHeapSize)=$(EmccInitialHeapSize) bytes. Set this msbuild property to change the value." Importance="High" />
     <Message Text="Linking with emcc with $(EmccLinkOptimizationFlag). This may take a while ..." Importance="High" />
     <Message Text="Running emcc with @(_EmccLinkStepArgs->'%(Identity)', ' ')" Importance="Low" />
-    <Exec Command='emcc "@$(_EmccDefaultFlagsRsp)" "@$(_EmccDefaultLinkFlagsRsp)" "@$(_EmccLinkRsp)"' EnvironmentVariables="@(EmscriptenEnvVars)" ConsoleToMSBuild="true">
+    <Exec Command='emcc "@$(_EmccDefaultFlagsRsp)" $(_EmccDefaultFlags) "@$(_EmccDefaultLinkFlagsRsp)" "@$(_EmccLinkRsp)"' EnvironmentVariables="@(EmscriptenEnvVars)" ConsoleToMSBuild="true">
       <Output TaskParameter="ConsoleOutput" PropertyName="_EmccLinkStepConsoleOutput" />
       <Output TaskParameter="ExitCode" PropertyName="_EmccLinkStepExitCode" />
     </Exec>
diff --git a/src/mono/wasm/runtime/CMakeLists.txt b/src/mono/wasm/runtime/CMakeLists.txt
index 6d76868952e0cd..6b8ef873ec27da 100644
--- a/src/mono/wasm/runtime/CMakeLists.txt
+++ b/src/mono/wasm/runtime/CMakeLists.txt
@@ -9,7 +9,7 @@ set(CMAKE_EXECUTABLE_SUFFIX ".js")
 add_executable(dotnet.native corebindings.c driver.c pinvoke.c)
 
 target_include_directories(dotnet.native PUBLIC ${MONO_INCLUDES} ${MONO_OBJ_INCLUDES} ${CMAKE_CURRENT_BINARY_DIR}/include/wasm)
-target_compile_options(dotnet.native PUBLIC @${NATIVE_BIN_DIR}/src/emcc-default.rsp @${NATIVE_BIN_DIR}/src/emcc-compile.rsp -DGEN_PINVOKE=1)
+target_compile_options(dotnet.native PUBLIC @${NATIVE_BIN_DIR}/src/emcc-default.rsp @${NATIVE_BIN_DIR}/src/emcc-compile.rsp -DGEN_PINVOKE=1 ${CONFIGURATION_COMPILE_OPTIONS})
 
 set_target_properties(dotnet.native PROPERTIES COMPILE_FLAGS ${CONFIGURATION_EMCC_FLAGS})
 
@@ -38,7 +38,7 @@ set_target_properties(dotnet.native PROPERTIES
     RUNTIME_OUTPUT_DIRECTORY "${NATIVE_BIN_DIR}")
 
 set(ignoreMeWasmOptFlags "${CONFIGURATION_WASM_OPT_FLAGS}")
-set(ignoreMeWasmOptAdditionalFlags "${WASM_OPT_ADDITIONAL_FLAGS}")
+set(ignoreMeWasmOptAdditionalFlags "${CONFIGURATION_COMPILE_OPTIONS}")
 set(ignoreMeEmsdkPath "${EMSDK_PATH}")
 
 if(CMAKE_BUILD_TYPE STREQUAL "Release")
diff --git a/src/mono/wasm/wasm.proj b/src/mono/wasm/wasm.proj
index c479a8cddf72e4..0b0f9fb7003234 100644
--- a/src/mono/wasm/wasm.proj
+++ b/src/mono/wasm/wasm.proj
@@ -270,7 +270,6 @@
     <ItemGroup>
       <_EmccLinkFlags Include="-s INITIAL_MEMORY=$(EmccInitialHeapSize)" />
       <_EmccLinkFlags Include="-s STACK_SIZE=$(EmccStackSize)" />
-      <_EmccCommonFlags Include="-msimd128" />
       <_EmccCommonFlags Condition="'$(MonoWasmThreads)' == 'true'" Include="-s USE_PTHREADS=1" />
       <_EmccLinkFlags Condition="'$(MonoWasmThreads)' == 'true'" Include="-Wno-pthreads-mem-growth" />
       <_EmccLinkFlags Condition="'$(MonoWasmThreads)' == 'true'" Include="-s PTHREAD_POOL_SIZE=0" />
@@ -372,6 +371,7 @@
       <CMakeConfigurationLinkFlags Condition="'$(Configuration)' == 'Release'">-O2</CMakeConfigurationLinkFlags>
 
       <CMakeConfigurationLinkFlags>$(CMakeConfigurationLinkFlags) -s EXPORT_ES6=1</CMakeConfigurationLinkFlags>
+      <CMakeConfigurationLinkFlags Condition="'$(WasmEnableSIMD)' == 'true'">$(CMakeConfigurationLinkFlags) -msimd128</CMakeConfigurationLinkFlags>
       <CMakeConfigurationLinkFlags Condition="'$(MonoWasmThreads)' == 'true'">$(CMakeConfigurationLinkFlags) -Wno-pthreads-mem-growth</CMakeConfigurationLinkFlags>
       <CMakeConfigurationLinkFlags                                            >$(CMakeConfigurationLinkFlags) --emit-symbol-map</CMakeConfigurationLinkFlags>
 
@@ -387,7 +387,7 @@
       <CMakeBuildRuntimeConfigureCmd>$(CMakeBuildRuntimeConfigureCmd) -DICU_LIB_DIR=&quot;$(ICULibDir.TrimEnd('\/').Replace('\','/'))&quot;</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd>$(CMakeBuildRuntimeConfigureCmd) -DMONO_ARTIFACTS_DIR=&quot;$(MonoArtifactsPath.TrimEnd('\/').Replace('\','/'))&quot;</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd>$(CMakeBuildRuntimeConfigureCmd) -DNATIVE_BIN_DIR=&quot;$(NativeBinDir.TrimEnd('\/').Replace('\','/'))&quot;</CMakeBuildRuntimeConfigureCmd>
-      <CMakeBuildRuntimeConfigureCmd Condition="'$(WasmEnableSIMD)' == 'true' and '$(Configuration)' == 'Release'">$(CMakeBuildRuntimeConfigureCmd) -DWASM_OPT_ADDITIONAL_FLAGS=&quot;--enable-simd&quot;</CMakeBuildRuntimeConfigureCmd>
+      <CMakeBuildRuntimeConfigureCmd Condition="'$(WasmEnableSIMD)' == 'true'">$(CMakeBuildRuntimeConfigureCmd) -DCONFIGURATION_COMPILE_OPTIONS=&quot;-msimd128&quot;</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd Condition="'$(MonoWasmThreads)' == 'true'">$(CMakeBuildRuntimeConfigureCmd) -DDISABLE_THREADS=0</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd Condition="'$(WasmEnableLegacyJsInterop)' == 'false'">$(CMakeBuildRuntimeConfigureCmd) -DDISABLE_LEGACY_JS_INTEROP=1</CMakeBuildRuntimeConfigureCmd>
       <CMakeBuildRuntimeConfigureCmd>$(CMakeBuildRuntimeConfigureCmd) $(CMakeConfigurationEmsdkPath)</CMakeBuildRuntimeConfigureCmd>