diff --git a/crates/ruff_cli/src/commands/check.rs b/crates/ruff_cli/src/commands/check.rs
index 001cb0ae8449de..7d63e299f4fa16 100644
--- a/crates/ruff_cli/src/commands/check.rs
+++ b/crates/ruff_cli/src/commands/check.rs
@@ -82,7 +82,7 @@ pub(crate) fn check(
 
                 let settings = resolver.resolve(path, pyproject_config);
 
-                if !resolved_file.is_root()
+                if (settings.file_resolver.force_exclude || !resolved_file.is_root())
                     && match_exclusion(
                         resolved_file.path(),
                         resolved_file.file_name(),
diff --git a/crates/ruff_cli/src/commands/check_stdin.rs b/crates/ruff_cli/src/commands/check_stdin.rs
index 67f01cd0e8d3a1..260da5a50135d6 100644
--- a/crates/ruff_cli/src/commands/check_stdin.rs
+++ b/crates/ruff_cli/src/commands/check_stdin.rs
@@ -18,17 +18,19 @@ pub(crate) fn check_stdin(
     noqa: flags::Noqa,
     fix_mode: flags::FixMode,
 ) -> Result<Diagnostics> {
-    if let Some(filename) = filename {
-        if !python_file_at_path(filename, pyproject_config, overrides)? {
-            return Ok(Diagnostics::default());
-        }
+    if pyproject_config.settings.file_resolver.force_exclude {
+        if let Some(filename) = filename {
+            if !python_file_at_path(filename, pyproject_config, overrides)? {
+                return Ok(Diagnostics::default());
+            }
 
-        let lint_settings = &pyproject_config.settings.linter;
-        if filename
-            .file_name()
-            .is_some_and(|name| match_exclusion(filename, name, &lint_settings.exclude))
-        {
-            return Ok(Diagnostics::default());
+            let lint_settings = &pyproject_config.settings.linter;
+            if filename
+                .file_name()
+                .is_some_and(|name| match_exclusion(filename, name, &lint_settings.exclude))
+            {
+                return Ok(Diagnostics::default());
+            }
         }
     }
     let package_root = filename.and_then(Path::parent).and_then(|path| {
diff --git a/crates/ruff_cli/src/commands/format.rs b/crates/ruff_cli/src/commands/format.rs
index 2d09472923552b..2db1338d4d9b01 100644
--- a/crates/ruff_cli/src/commands/format.rs
+++ b/crates/ruff_cli/src/commands/format.rs
@@ -117,14 +117,14 @@ pub(crate) fn format(
                         return None;
                     };
 
-                    let resolved_settings = resolver.resolve(path, &pyproject_config);
+                    let settings = resolver.resolve(path, &pyproject_config);
 
                     // Ignore files that are excluded from formatting
-                    if !resolved_file.is_root()
+                    if (settings.file_resolver.force_exclude || !resolved_file.is_root())
                         && match_exclusion(
                             path,
                             resolved_file.file_name(),
-                            &resolved_settings.formatter.exclude,
+                            &settings.formatter.exclude,
                         )
                     {
                         return None;
@@ -139,13 +139,7 @@ pub(crate) fn format(
 
                     Some(
                         match catch_unwind(|| {
-                            format_path(
-                                path,
-                                &resolved_settings.formatter,
-                                source_type,
-                                mode,
-                                cache,
-                            )
+                            format_path(path, &settings.formatter, source_type, mode, cache)
                         }) {
                             Ok(inner) => inner.map(|result| FormatPathResult {
                                 path: resolved_file.path().to_path_buf(),
diff --git a/crates/ruff_cli/src/commands/format_stdin.rs b/crates/ruff_cli/src/commands/format_stdin.rs
index 082dfedfb00daa..032ece074ad71f 100644
--- a/crates/ruff_cli/src/commands/format_stdin.rs
+++ b/crates/ruff_cli/src/commands/format_stdin.rs
@@ -31,17 +31,19 @@ pub(crate) fn format_stdin(cli: &FormatArguments, overrides: &CliOverrides) -> R
 
     let mode = FormatMode::from_cli(cli);
 
-    if let Some(filename) = cli.stdin_filename.as_deref() {
-        if !python_file_at_path(filename, &pyproject_config, overrides)? {
-            return Ok(ExitStatus::Success);
-        }
+    if pyproject_config.settings.file_resolver.force_exclude {
+        if let Some(filename) = cli.stdin_filename.as_deref() {
+            if !python_file_at_path(filename, &pyproject_config, overrides)? {
+                return Ok(ExitStatus::Success);
+            }
 
-        let format_settings = &pyproject_config.settings.formatter;
-        if filename
-            .file_name()
-            .is_some_and(|name| match_exclusion(filename, name, &format_settings.exclude))
-        {
-            return Ok(ExitStatus::Success);
+            let format_settings = &pyproject_config.settings.formatter;
+            if filename
+                .file_name()
+                .is_some_and(|name| match_exclusion(filename, name, &format_settings.exclude))
+            {
+                return Ok(ExitStatus::Success);
+            }
         }
     }
 
diff --git a/crates/ruff_workspace/src/resolver.rs b/crates/ruff_workspace/src/resolver.rs
index 1f57a1504eba3e..fc12feaad3ace0 100644
--- a/crates/ruff_workspace/src/resolver.rs
+++ b/crates/ruff_workspace/src/resolver.rs
@@ -483,10 +483,6 @@ pub fn python_file_at_path(
     pyproject_config: &PyprojectConfig,
     transformer: &dyn ConfigurationTransformer,
 ) -> Result<bool> {
-    if !pyproject_config.settings.file_resolver.force_exclude {
-        return Ok(true);
-    }
-
     // Normalize the path (e.g., convert from relative to absolute).
     let path = fs::normalize_path(path);