diff --git a/onnxruntime/core/framework/session_options.h b/onnxruntime/core/framework/session_options.h
index 40c59cfcf6..796a018ac0 100644
--- a/onnxruntime/core/framework/session_options.h
+++ b/onnxruntime/core/framework/session_options.h
@@ -65,6 +65,11 @@ struct FreeDimensionOverride {
  * Configuration information for a session.
  */
 struct SessionOptions {
+#if defined(__wasm__) && defined(__EMSCRIPTEN_PTHREADS__)
+  static constexpr bool DEFAULT_USE_PER_SESSION_THREADS = false;
+#else
+  static constexpr bool DEFAULT_USE_PER_SESSION_THREADS = true;
+#endif
   ExecutionMode execution_mode = ExecutionMode::ORT_SEQUENTIAL;
 
   // set the execution order of the graph
@@ -129,7 +134,8 @@ struct SessionOptions {
 
   // By default the session uses its own set of threadpools, unless this is set to false.
   // Use this in conjunction with the CreateEnvWithGlobalThreadPools API.
-  bool use_per_session_threads = true;
+  bool use_per_session_threads = DEFAULT_USE_PER_SESSION_THREADS;
+
   bool thread_pool_allow_spinning = true;
 
   // Deterministic compute is likely not as performant. This option is default to false.
diff --git a/onnxruntime/test/framework/inference_session_test.cc b/onnxruntime/test/framework/inference_session_test.cc
index 486ec37d1e..2522ee3b49 100644
--- a/onnxruntime/test/framework/inference_session_test.cc
+++ b/onnxruntime/test/framework/inference_session_test.cc
@@ -578,6 +578,9 @@ TEST(InferenceSessionTests, ModelMetadata) {
 }
 #endif
 TEST(InferenceSessionTests, CheckRunLogger) {
+  if constexpr (!SessionOptions::DEFAULT_USE_PER_SESSION_THREADS) {
+    GTEST_SKIP() << "Skipping the test";
+  }
   SessionOptions so;
 
   so.session_logid = "CheckRunLogger";
@@ -837,6 +840,9 @@ TEST(InferenceSessionTests, PreAllocateOutputVector) {
 }
 
 TEST(InferenceSessionTests, ConfigureVerbosityLevel) {
+  if constexpr (!SessionOptions::DEFAULT_USE_PER_SESSION_THREADS) {
+    GTEST_SKIP() << "Skipping the test";
+  }
   SessionOptions so;
 
   so.session_logid = "ConfigureVerbosityLevel";
@@ -2661,6 +2667,9 @@ class InferenceSessionTestSharingAllocator : public InferenceSessionWrapper {
 
 // Ensure sessions use the same allocator. It uses ORT created allocator.
 TEST(InferenceSessionTests, AllocatorSharing_EnsureSessionsUseSameOrtCreatedAllocator) {
+  if constexpr (!SessionOptions::DEFAULT_USE_PER_SESSION_THREADS) {
+    GTEST_SKIP() << "Skipping the test";
+  }
   auto logging_manager = std::make_unique<logging::LoggingManager>(
       std::unique_ptr<ISink>(new CLogSink()), logging::Severity::kVERBOSE, false,
       LoggingManager::InstanceType::Temporal);
@@ -2706,6 +2715,9 @@ TEST(InferenceSessionTests, AllocatorSharing_EnsureSessionsUseSameOrtCreatedAllo
 
 // Ensure sessions don't use the same allocator. It uses ORT created allocator.
 TEST(InferenceSessionTests, AllocatorSharing_EnsureSessionsDontUseSameOrtCreatedAllocator) {
+  if constexpr (!SessionOptions::DEFAULT_USE_PER_SESSION_THREADS) {
+    GTEST_SKIP() << "Skipping the test";
+  }
   auto logging_manager = std::make_unique<logging::LoggingManager>(
       std::unique_ptr<ISink>(new CLogSink()), logging::Severity::kVERBOSE, false,
       LoggingManager::InstanceType::Temporal);
@@ -2758,6 +2770,9 @@ class InferenceSessionTestSharingInitializer : public InferenceSessionWrapper {
 };
 
 TEST(InferenceSessionTests, InitializerSharing_EnsureSessionsUseUserAddedInitializer) {
+  if constexpr (!SessionOptions::DEFAULT_USE_PER_SESSION_THREADS) {
+    GTEST_SKIP() << "Skipping the test";
+  }
   auto logging_manager = std::make_unique<logging::LoggingManager>(
       std::unique_ptr<ISink>(new CLogSink()), logging::Severity::kVERBOSE, false,
       LoggingManager::InstanceType::Temporal);
@@ -2942,6 +2957,9 @@ TEST(InferenceSessionTests, GlobalThreadPoolWithDenormalAsZero) {
 
 // test inter thread pool with setting denormal as zero
 TEST(InferenceSessionTests, InterThreadPoolWithDenormalAsZero) {
+  if constexpr (!SessionOptions::DEFAULT_USE_PER_SESSION_THREADS) {
+    GTEST_SKIP() << "Skipping the test";
+  }
   // test if denormal-as-zero mode is supported
   if (!SetDenormalAsZero(false)) {
     return;
diff --git a/onnxruntime/test/providers/cpu/activation/activation_op_test.cc b/onnxruntime/test/providers/cpu/activation/activation_op_test.cc
index 7ec9e0f345..ddb0a66206 100644
--- a/onnxruntime/test/providers/cpu/activation/activation_op_test.cc
+++ b/onnxruntime/test/providers/cpu/activation/activation_op_test.cc
@@ -588,6 +588,9 @@ TEST_F(ActivationOpTest, Softplus) {
 }
 
 TEST_F(ActivationOpNoInfTest, Softsign) {
+  if constexpr (!SessionOptions::DEFAULT_USE_PER_SESSION_THREADS) {
+    GTEST_SKIP() << "Skipping the test";
+  }
   // TODO: Unskip when fixed #41968513
   if (DefaultDmlExecutionProvider().get() != nullptr) {
     GTEST_SKIP() << "Skipping because of the following error: The difference between expected[i] and output[i] is 1, which exceeds threshold";