diff --git a/CHANGELOG.md b/CHANGELOG.md
index 876251e27..fa0d572ff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@
 
 - allow mixed `str` and `dict` entries in lint config ([#3228](https://github.com/nf-core/tools/pull/3228))
 - fix meta_yml linting test failing due to module.process_name always being "" ([#3317](https://github.com/nf-core/tools/pull/3317))
+- fix module section regex matching wrong things ([#3321](https://github.com/nf-core/tools/pull/3321))
 
 ### Modules
 
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 9a1790aeb..ba3b87f79 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -96,19 +96,19 @@ def main_nf(
     for line in iter_lines:
         if re.search(r"^\s*process\s*\w*\s*{", line) and state == "module":
             state = "process"
-        if re.search(r"input\s*:", line) and state in ["process"]:
+        if re.search(r"^\s*input\s*:", line) and state in ["process"]:
             state = "input"
             continue
-        if re.search(r"output\s*:", line) and state in ["input", "process"]:
+        if re.search(r"^\s*output\s*:", line) and state in ["input", "process"]:
             state = "output"
             continue
-        if re.search(r"when\s*:", line) and state in ["input", "output", "process"]:
+        if re.search(r"^\s*when\s*:", line) and state in ["input", "output", "process"]:
             state = "when"
             continue
-        if re.search(r"script\s*:", line) and state in ["input", "output", "when", "process"]:
+        if re.search(r"^\s*script\s*:", line) and state in ["input", "output", "when", "process"]:
             state = "script"
             continue
-        if re.search(r"shell\s*:", line) and state in ["input", "output", "when", "process"]:
+        if re.search(r"^\s*shell\s*:", line) and state in ["input", "output", "when", "process"]:
             state = "shell"
             continue