diff --git a/CHANGELOG.md b/CHANGELOG.md
index d46348e2db..74b5f00fd5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@
 
 - accept `process_low_memory` as a standard module label ([#4264](https://github.com/nf-core/tools/pull/4264))
 - improve linting for `modules.json` to add support for only installing subworkflows from a repository and provide more explicit error messages ([#4287](https://github.com/nf-core/tools/pull/4287))
+- Replace `ext.when` linting to disallow use ([#4314](https://github.com/nf-core/tools/pull/4314))
 
 ### Modules
 
diff --git a/nf_core/module-template/main.nf b/nf_core/module-template/main.nf
index ac40bb511f..3a5a7e59af 100644
--- a/nf_core/module-template/main.nf
+++ b/nf_core/module-template/main.nf
@@ -72,9 +72,6 @@ process {{ component_name_underscore|upper }} {
     {%- endif %}
     tuple val("${task.process}"), val('{{ component }}'), eval("{{ component }} --version"), topic: versions, emit: versions_{{ component }}
 
-    when:
-    task.ext.when == null || task.ext.when
-
     script:
     def args = task.ext.args ?: ''
     {% if has_meta -%}
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index b589bc3f0c..42157c311b 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -341,22 +341,33 @@ def check_script_section(self, lines):
 
 def check_when_section(self, lines):
     """
-    Lint the when: section
-    Checks whether the line is modified from 'task.ext.when == null || task.ext.when'
+    Lint the when: section.
+
+    The module template no longer allows `task.ext.when` in `when:` blocks.
     """
     if len(lines) == 0:
-        self.failed.append(("main_nf", "when_exist", "when: condition has been removed", self.main_nf))
-        return
-    if len(lines) > 1:
-        self.failed.append(("main_nf", "when_exist", "when: condition has too many lines", self.main_nf))
+        self.passed.append(("main_nf", "when_exist", "No when: condition found", self.main_nf))
         return
     self.passed.append(("main_nf", "when_exist", "when: condition is present", self.main_nf))
 
-    # Check the condition hasn't been changed.
-    if lines[0].strip() != "task.ext.when == null || task.ext.when":
-        self.failed.append(("main_nf", "when_condition", "when: condition has been altered", self.main_nf))
+    if any("task.ext.when" in line for line in lines):
+        self.failed.append(
+            (
+                "main_nf",
+                "when_condition",
+                "task.ext.when is no longer allowed in when: condition",
+                self.main_nf,
+            )
+        )
         return
-    self.passed.append(("main_nf", "when_condition", "when: condition is unchanged", self.main_nf))
+    self.passed.append(
+        (
+            "main_nf",
+            "when_condition",
+            "when: condition does not use task.ext.when",
+            self.main_nf,
+        )
+    )
 
 
 def check_process_section(self, lines, registry, fix_version, progress_bar):
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index f6c3848f71..a5344e1cce 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -7,6 +7,7 @@
     check_container_link_line,
     check_process_labels,
     check_script_section,
+    check_when_section,
 )
 
 from ...test_modules import TestModules
@@ -101,6 +102,26 @@ def test_container_links(content, passed, warned, failed):
     assert len(mock_lint.failed) == failed
 
 
+def test_when_section_rejects_task_ext_when():
+    """Test that task.ext.when in a when: block fails linting"""
+    mock_lint = MockModuleLint()
+
+    check_when_section(mock_lint, ["task.ext.when == null || task.ext.when"])
+
+    assert len(mock_lint.failed) == 1
+    assert "task.ext.when" in mock_lint.failed[0][2]
+
+
+def test_when_section_allows_missing_when_block():
+    """Test that modules without a when: block pass this lint"""
+    mock_lint = MockModuleLint()
+
+    check_when_section(mock_lint, [])
+
+    assert len(mock_lint.failed) == 0
+    assert any("No when: condition found" in message for _, _, message, _ in mock_lint.passed)
+
+
 class TestMainNfLinting(TestModules):
     """
     Test main.nf linting functionality.