diff --git a/pyodide_build/cli/xbuildenv.py b/pyodide_build/cli/xbuildenv.py
index ab1806f0..230b86ab 100644
--- a/pyodide_build/cli/xbuildenv.py
+++ b/pyodide_build/cli/xbuildenv.py
@@ -232,4 +232,3 @@ def _install_emscripten(
     emsdk_dir = manager.install_emscripten(version)
 
     print("Installing emsdk complete.")
-    print(f"Use `source {emsdk_dir}/emsdk_env.sh` to set up the environment.")
diff --git a/pyodide_build/tests/test_cli_install_emscripten.py b/pyodide_build/tests/test_cli_install_emscripten.py
index 78674176..12e9685e 100644
--- a/pyodide_build/tests/test_cli_install_emscripten.py
+++ b/pyodide_build/tests/test_cli_install_emscripten.py
@@ -60,8 +60,6 @@ def fake_install(self, version):
     assert result.exit_code == 0, result.stdout
     assert "Installing emsdk..." in result.stdout, result.stdout
     assert "Installing emsdk complete." in result.stdout, result.stdout
-    assert "Use `source" in result.stdout, result.stdout
-    assert "emsdk_env.sh` to set up the environment." in result.stdout, result.stdout
     assert called["version"] == "3.1.46"
 
 
@@ -134,7 +132,6 @@ def fake_install(self, version):
     assert result.exit_code == 0, result.stdout
     assert "Installing emsdk..." in result.stdout, result.stdout
     assert "Installing emsdk complete." in result.stdout, result.stdout
-    assert str(existing_emsdk / "emsdk_env.sh") in result.stdout
 
 
 def test_install_emscripten_git_failure(tmp_path, monkeypatch):
@@ -220,5 +217,3 @@ def test_install_emscripten_output_format(tmp_path, monkeypatch):
     # Verify output format - check for key messages (logger adds extra lines)
     assert "Installing emsdk..." in result.stdout
     assert "Installing emsdk complete." in result.stdout
-    assert "Use `source" in result.stdout
-    assert "emsdk_env.sh` to set up the environment." in result.stdout
diff --git a/pyodide_build/tests/test_install_emscripten.py b/pyodide_build/tests/test_install_emscripten.py
index d0054476..dd1ab6d0 100644
--- a/pyodide_build/tests/test_install_emscripten.py
+++ b/pyodide_build/tests/test_install_emscripten.py
@@ -113,9 +113,9 @@ def mock_run_side_effect(cmd, **kwargs):
 
     # Verify
     assert result == emsdk_dir
-    assert mock_run.call_count == 4  # clone + install + patch + activate
+    assert mock_run.call_count == 5  # clone + install + patch + activate + source env
 
-    # Check the four subprocess calls
+    # Check the subprocess calls in the expected order
     calls = mock_run.call_args_list
 
     # 1. Clone emsdk
@@ -153,6 +153,14 @@ def mock_run_side_effect(cmd, **kwargs):
         check=True,
     )
 
+    # 5. Source the environment script to validate activation
+    assert calls[4] == call(
+        "source ./emsdk_env.sh",
+        check=True,
+        shell=True,
+        cwd=emsdk_dir,
+    )
+
 
 def test_install_emscripten_specific_version(tmp_path, monkeypatch):
     """Test installing a specific Emscripten SDK version"""
@@ -182,7 +190,7 @@ def mock_run_side_effect(cmd, **kwargs):
 
     # Verify
     assert result == emsdk_dir
-    assert mock_run.call_count == 4  # clone + install + patch + activate
+    assert mock_run.call_count == 5  # clone + install + patch + activate + source env
 
     calls = mock_run.call_args_list
 
@@ -208,6 +216,14 @@ def mock_run_side_effect(cmd, **kwargs):
         check=True,
     )
 
+    # Verify sourcing of the environment script (call 4)
+    assert calls[4] == call(
+        "source ./emsdk_env.sh",
+        check=True,
+        shell=True,
+        cwd=emsdk_dir,
+    )
+
 
 def test_install_emscripten_with_existing_emsdk(tmp_path, monkeypatch):
     """Test installing Emscripten when emsdk directory already exists"""
@@ -234,7 +250,7 @@ def test_install_emscripten_with_existing_emsdk(tmp_path, monkeypatch):
 
     # Verify - should pull, then install, patch, and activate
     assert result == emsdk_dir
-    assert mock_run.call_count == 4
+    assert mock_run.call_count == 5
 
     calls = mock_run.call_args_list
 
@@ -261,6 +277,14 @@ def test_install_emscripten_with_existing_emsdk(tmp_path, monkeypatch):
         check=True,
     )
 
+    # 5. Source the environment script
+    assert calls[4] == call(
+        "source ./emsdk_env.sh",
+        check=True,
+        shell=True,
+        cwd=emsdk_dir,
+    )
+
 
 def test_install_emscripten_patch_fails(tmp_path, monkeypatch):
     """Test handling of patch application failure due to version mismatch"""
diff --git a/pyodide_build/xbuildenv.py b/pyodide_build/xbuildenv.py
index 745172e9..a9a71144 100644
--- a/pyodide_build/xbuildenv.py
+++ b/pyodide_build/xbuildenv.py
@@ -520,6 +520,19 @@ def install_emscripten(self, emscripten_version: str = "latest") -> Path:
         )
 
         logger.info("Emscripten SDK installed successfully at %s", emsdk_dir)
+
+        try:
+            subprocess.run(
+                "source ./emsdk_env.sh",
+                check=True,
+                shell=True,
+                cwd=emsdk_dir,
+            )
+        except subprocess.CalledProcessError as e:
+            raise RuntimeError(
+                f"Failed to activate emsdk environment. Please check the emsdk installation at {emsdk_dir}"
+            ) from e
+
         return emsdk_dir
 
     def _add_version_marker(self) -> None: