diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3f46a265cc..6dd09482b1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@
 
 ### Linting
 
+- Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
+
 ### Download
 
 ### Components
diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py
index d801caf704..0c87100622 100644
--- a/nf_core/lint/files_exist.py
+++ b/nf_core/lint/files_exist.py
@@ -200,8 +200,8 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
         Path("Singularity"),
     ]
     files_warn_ifexists = [Path(".travis.yml")]
-    files_fail_ifinconfig: List[Tuple[Path, Dict[str, str]]] = [
-        (Path("lib", "nfcore_external_java_deps.jar"), {"plugins": "nf-validation"}),
+    files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = [
+        (Path("lib", "nfcore_external_java_deps.jar"), [{"plugins": "nf-validation"}, {"plugins": "nf-schema"}]),
     ]
 
     # Remove files that should be ignored according to the linting config
@@ -246,10 +246,11 @@ def pf(file_path: Union[str, Path]) -> Path:
         if str(file_cond[0]) in ignore_files:
             continue
         in_config = False
-        config_key, config_value = list(file_cond[1].items())[0]
-        if config_key in self.nf_config and config_value in self.nf_config[config_key]:
-            log.debug(f"Found {config_key} in nextflow.config with value {config_value}")
-            in_config = True
+        for condition in file_cond[1]:
+            config_key, config_value = list(condition.items())[0]
+            if config_key in self.nf_config and config_value in self.nf_config[config_key]:
+                log.debug(f"Found {config_key} in nextflow.config with value {config_value}")
+                in_config = True
         if pf(file_cond[0]).is_file() and in_config:
             failed.append(f"File must be removed: {self._wrap_quotes(file_cond[0])}")
         elif pf(file_cond[0]).is_file() and not in_config:
diff --git a/tests/lint/files_exist.py b/tests/lint/files_exist.py
index 5081522899..08da7f14db 100644
--- a/tests/lint/files_exist.py
+++ b/tests/lint/files_exist.py
@@ -79,3 +79,20 @@ def test_files_exist_fail_conditional(self):
     results = lint_obj.files_exist()
     assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
     assert results["ignored"] == []
+
+
+def test_files_exist_pass_conditional_nfschema(self):
+    new_pipeline = self._make_pipeline_copy()
+    # replace nf-validation with nf-schema in nextflow.config
+    with open(Path(new_pipeline, "nextflow.config")) as f:
+        config = f.read()
+    config = config.replace("nf-validation", "nf-schema")
+    with open(Path(new_pipeline, "nextflow.config"), "w") as f:
+        f.write(config)
+
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    lint_obj.nf_config["manifest.schema"] = "nf-core"
+    results = lint_obj.files_exist()
+    assert results["failed"] == []
+    assert results["ignored"] == []
diff --git a/tests/test_lint.py b/tests/test_lint.py
index b72a6bfdfa..15c1550e72 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -212,6 +212,7 @@ def test_sphinx_md_files(self):
         test_files_exist_missing_main,
         test_files_exist_pass,
         test_files_exist_pass_conditional,
+        test_files_exist_pass_conditional_nfschema,
     )
     from .lint.files_unchanged import (  # type: ignore[misc]
         test_files_unchanged_fail,