diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2bfd0400a4..b1f0d17153 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
 ### Linting
 
 - 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))
 
 ### Modules
 
diff --git a/nf_core/pipelines/lint/modules_json.py b/nf_core/pipelines/lint/modules_json.py
index f7f5a077e7..8fa09b379b 100644
--- a/nf_core/pipelines/lint/modules_json.py
+++ b/nf_core/pipelines/lint/modules_json.py
@@ -25,32 +25,32 @@ def modules_json(self) -> dict[str, list[str]]:
         all_modules_passed = True
 
         for repo in modules_json_dict["repos"]:
-            # Check if the modules.json has been updated to keep the
-            if "modules" not in modules_json_dict["repos"][repo] or not repo.startswith("http"):
-                failed.append(
-                    "Your `modules.json` file is outdated. "
-                    "It will be automatically generated by running any module command."
-                )
-                continue
-
-            for install_dir in modules_json_dict["repos"][repo]["modules"]:
-                for module, module_entry in modules_json_dict["repos"][repo]["modules"][install_dir].items():
-                    if not Path(modules_dir, install_dir, module).exists():
-                        failed.append(
-                            f"Entry for `{Path(modules_dir, install_dir, module)}` found in `modules.json` but module is not installed in "
-                            "pipeline."
-                        )
-                        all_modules_passed = False
-                    if module_entry.get("branch") is None:
-                        failed.append(
-                            f"Entry for `{Path(modules_dir, install_dir, module)}` is missing branch information."
-                        )
-                    if module_entry.get("git_sha") is None:
-                        failed.append(
-                            f"Entry for `{Path(modules_dir, install_dir, module)}` is missing version information."
-                        )
-        if all_modules_passed:
-            passed.append("Only installed modules found in `modules.json`")
+            if not repo.startswith("http"):
+                failed.append(f'Repository link for {repo} doesn\'t start with "http" in `modules.json`.')
+
+            if "modules" in modules_json_dict["repos"][repo]:
+                # Module linting
+                for install_dir in modules_json_dict["repos"][repo]["modules"]:
+                    for module, module_entry in modules_json_dict["repos"][repo]["modules"][install_dir].items():
+                        if not Path(modules_dir, install_dir, module).exists():
+                            failed.append(
+                                f"Entry for `{Path(modules_dir, install_dir, module)}` found in `modules.json` but module is not installed in "
+                                "pipeline."
+                            )
+                            all_modules_passed = False
+                        if module_entry.get("branch") is None:
+                            failed.append(
+                                f"Entry for `{Path(modules_dir, install_dir, module)}` is missing branch information."
+                            )
+                        if module_entry.get("git_sha") is None:
+                            failed.append(
+                                f"Entry for `{Path(modules_dir, install_dir, module)}` is missing version information."
+                            )
+                if all_modules_passed:
+                    passed.append("Only installed modules found in `modules.json`")
+
+            if not any(component in modules_json_dict["repos"][repo] for component in ["modules", "subworkflows"]):
+                failed.append(f"No modules or subworkflows installed for {repo} in `modules.json`.")
     else:
         warned.append("Could not open `modules.json` file.")
 
diff --git a/tests/pipelines/lint/test_modules_json.py b/tests/pipelines/lint/test_modules_json.py
index 0d8333d9a2..6e72930009 100644
--- a/tests/pipelines/lint/test_modules_json.py
+++ b/tests/pipelines/lint/test_modules_json.py
@@ -1,10 +1,74 @@
+import json
+
+from nf_core.modules.modules_json import (
+    ModulesJson,
+    ModulesJsonType,
+)
+
 from ..test_lint import TestLint
 
 
 class TestLintModulesJson(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self._modules_json_object: ModulesJson = ModulesJson(self.pipeline_dir)
+        self._modules_json_object.load()
+        self.modules_json_path = self._modules_json_object.modules_json_path
+        assert self._modules_json_object.modules_json is not None
+        self.modules_json: ModulesJsonType = self._modules_json_object.modules_json
+
+    def _update_modules_json(self, new_modules_json) -> None:
+        # Update modules_json so that it is concordant at all levels of the class
+        self.modules_json = new_modules_json
+        self._modules_json_object.modules_json = new_modules_json
+        with open(self.modules_json_path, "w") as modules_json_file:
+            json.dump(new_modules_json, modules_json_file)
+
     def test_modules_json_pass(self):
         self.lint_obj._load()
         results = self.lint_obj.modules_json()
         assert len(results.get("warned", [])) == 0
         assert len(results.get("failed", [])) == 0
         assert len(results.get("passed", [])) > 0
+
+    def test_modules_json_with_repo_not_starting_with_http_fail(self):
+        # Change the link of the first repo in modules_json to not start with "http"
+        new_modules_json = self.modules_json
+        first_repo = next(iter(new_modules_json["repos"]))
+        new_modules_json["repos"]["incorrect_repo_link"] = new_modules_json["repos"].pop(first_repo)
+
+        self._update_modules_json(new_modules_json)
+
+        # Check linting results
+        results = self.lint_obj.modules_json()
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 1
+        assert len(results.get("passed", [])) == 1  # The repository still contains only installed modules
+
+    def test_modules_json_with_only_subworkflow_entries(self):
+        # Keep only "subworkflows" in the first repo in modules_json
+        new_modules_json = self.modules_json
+        first_repo = next(iter(new_modules_json["repos"]))
+        new_modules_json["repos"][first_repo] = {"subworkflows": new_modules_json["repos"][first_repo]["subworkflows"]}
+
+        self._update_modules_json(new_modules_json)
+
+        # Check linting results
+        results = self.lint_obj.modules_json()
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("passed", [])) == 0  # There is no subworkflow linting so no "passed" is returned
+
+    def test_modules_json_with_repo_with_no_modules_or_subworkflows_fail(self):
+        # Change the first repo in modules_json to have no modules or subworkflows
+        new_modules_json = self.modules_json
+        first_repo = next(iter(new_modules_json["repos"]))
+        new_modules_json["repos"][first_repo] = {}
+
+        self._update_modules_json(new_modules_json)
+
+        # Check linting results
+        results = self.lint_obj.modules_json()
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 1
+        assert len(results.get("passed", [])) == 0