diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
index 52463f6e1..a9c6a0751 100644
--- a/.github/workflows/nightly.yml
+++ b/.github/workflows/nightly.yml
@@ -512,11 +512,10 @@ jobs:
         run: |
           source ~/emsdk/emsdk_env.sh
           cd src/api/python
-          CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" CXXFLAGS="${CXXFLAGS}" ~/env/bin/pyodide build --exports whole_archive
-        env:
-          CFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0 -g2"
-          LDFLAGS: "-fexceptions -s WASM_BIGINT"
-          CXXFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0"
+          # Exception/longjmp/bigint flags are declared in pyproject.toml and
+          # combined with Pyodide's -fwasm-exceptions defaults. Passing the
+          # legacy JS-EH -fexceptions flags here conflicts with the wasm-EH ABI.
+          ~/env/bin/pyodide build --exports whole_archive
 
       - name: Setup env-pyodide
         run: |
diff --git a/.github/workflows/pyodide.yml b/.github/workflows/pyodide.yml
index 16f54f824..4f785f1ca 100644
--- a/.github/workflows/pyodide.yml
+++ b/.github/workflows/pyodide.yml
@@ -42,11 +42,10 @@ jobs:
       run: |
          source ~/emsdk/emsdk_env.sh 
          cd src/api/python 
-         CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" CXXFLAG="${CXXFLAGS}" ~/env/bin/pyodide build --exports whole_archive
-      env:
-         CFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0 -g2"
-         LDFLAGS: "-fexceptions -s WASM_BIGINT"     
-         CXXFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0"
+         # Exception/longjmp/bigint flags are declared in pyproject.toml and
+         # combined with Pyodide's -fwasm-exceptions defaults. Passing the
+         # legacy JS-EH -fexceptions flags here conflicts with the wasm-EH ABI.
+         ~/env/bin/pyodide build --exports whole_archive
          
     - name: Setup env-pyodide
       run: |
@@ -65,4 +64,3 @@ jobs:
           name: pyodide-wheel
           path: src/api/python/dist/*.whl
           retention-days: 1         
-
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f92f7a2d5..147e150c4 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -522,11 +522,10 @@ jobs:
         run: |
           source ~/emsdk/emsdk_env.sh
           cd src/api/python
-          CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" CXXFLAGS="${CXXFLAGS}" ~/env/bin/pyodide build --exports whole_archive
-        env:
-          CFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0 -g2"
-          LDFLAGS: "-fexceptions -s WASM_BIGINT"
-          CXXFLAGS: "-fexceptions -s DISABLE_EXCEPTION_CATCHING=0"
+          # Exception/longjmp/bigint flags are declared in pyproject.toml and
+          # combined with Pyodide's -fwasm-exceptions defaults. Passing the
+          # legacy JS-EH -fexceptions flags here conflicts with the wasm-EH ABI.
+          ~/env/bin/pyodide build --exports whole_archive
 
       - name: Setup env-pyodide
         run: |