diff --git a/.changeset/fix-changed-deleted-file.md b/.changeset/fix-changed-deleted-file.md
new file mode 100644
index 000000000000..5b34024bb8c9
--- /dev/null
+++ b/.changeset/fix-changed-deleted-file.md
@@ -0,0 +1,5 @@
+---
+"@biomejs/biome": patch
+---
+
+Fix `--changed` and `--staged` flags throwing "No such file or directory" error when a file has been deleted or renamed in the working directory. The CLI now filters out files that no longer exist before processing.
diff --git a/crates/biome_cli/src/changed.rs b/crates/biome_cli/src/changed.rs
index b850ebb54de3..f6085cd9ab3a 100644
--- a/crates/biome_cli/src/changed.rs
+++ b/crates/biome_cli/src/changed.rs
@@ -1,6 +1,7 @@
 use crate::CliDiagnostic;
 use biome_configuration::Configuration;
 use biome_fs::FileSystem;
+use camino::Utf8Path;
 use std::ffi::OsString;
 
 pub(crate) fn get_changed_files(
@@ -26,7 +27,12 @@ pub(crate) fn get_changed_files(
 
     let changed_files = fs.get_changed_files(base)?;
 
-    let filtered_changed_files = changed_files.iter().map(OsString::from).collect::<Vec<_>>();
+    // Filter out files that no longer exist (e.g., deleted or renamed in the working directory)
+    let filtered_changed_files = changed_files
+        .iter()
+        .filter(|file| fs.path_is_file(Utf8Path::new(file)))
+        .map(OsString::from)
+        .collect::<Vec<_>>();
 
     Ok(filtered_changed_files)
 }
@@ -34,7 +40,12 @@ pub(crate) fn get_changed_files(
 pub(crate) fn get_staged_files(fs: &dyn FileSystem) -> Result<Vec<OsString>, CliDiagnostic> {
     let staged_files = fs.get_staged_files()?;
 
-    let filtered_staged_files = staged_files.iter().map(OsString::from).collect::<Vec<_>>();
+    // Filter out files that no longer exist (e.g., deleted or renamed in the working directory)
+    let filtered_staged_files = staged_files
+        .iter()
+        .filter(|file| fs.path_is_file(Utf8Path::new(file)))
+        .map(OsString::from)
+        .collect::<Vec<_>>();
 
     Ok(filtered_staged_files)
 }
diff --git a/crates/biome_cli/tests/commands/lint.rs b/crates/biome_cli/tests/commands/lint.rs
index a9a734160715..cd7205495063 100644
--- a/crates/biome_cli/tests/commands/lint.rs
+++ b/crates/biome_cli/tests/commands/lint.rs
@@ -3665,6 +3665,76 @@ fn should_error_if_unchanged_files_only_with_changed_flag() {
     ));
 }
 
+#[test]
+fn should_skip_nonexistent_changed_files() {
+    let mut console = BufferConsole::default();
+    let mut fs = MemoryFileSystem::default();
+
+    // Git reports "deleted.js" as changed, but it doesn't exist in the working directory
+    fs.set_on_get_changed_files(Box::new(|| {
+        vec![String::from("exists.js"), String::from("deleted.js")]
+    }));
+
+    // Only "exists.js" exists in the file system
+    fs.insert(
+        Utf8Path::new("exists.js").into(),
+        r#"console.log('exists');"#.as_bytes(),
+    );
+    // Note: "deleted.js" is NOT inserted - simulating a deleted file
+
+    let (fs, result) = run_cli(
+        fs,
+        &mut console,
+        Args::from(["lint", "--changed", "--since=main"].as_slice()),
+    );
+
+    // Should succeed without "No such file or directory" error
+    assert!(result.is_ok(), "run_cli returned {result:?}");
+
+    assert_cli_snapshot(SnapshotPayload::new(
+        module_path!(),
+        "should_skip_nonexistent_changed_files",
+        fs,
+        console,
+        result,
+    ));
+}
+
+#[test]
+fn should_skip_nonexistent_staged_files() {
+    let mut console = BufferConsole::default();
+    let mut fs = MemoryFileSystem::default();
+
+    // Git reports "deleted.js" as staged, but it doesn't exist in the working directory
+    fs.set_on_get_staged_files(Box::new(|| {
+        vec![String::from("exists.js"), String::from("deleted.js")]
+    }));
+
+    // Only "exists.js" exists in the file system
+    fs.insert(
+        Utf8Path::new("exists.js").into(),
+        r#"console.log('exists');"#.as_bytes(),
+    );
+    // Note: "deleted.js" is NOT inserted - simulating a deleted file
+
+    let (fs, result) = run_cli(
+        fs,
+        &mut console,
+        Args::from(["lint", "--staged"].as_slice()),
+    );
+
+    // Should succeed without "No such file or directory" error
+    assert!(result.is_ok(), "run_cli returned {result:?}");
+
+    assert_cli_snapshot(SnapshotPayload::new(
+        module_path!(),
+        "should_skip_nonexistent_staged_files",
+        fs,
+        console,
+        result,
+    ));
+}
+
 #[test]
 fn linter_shows_the_default_severity_of_rule_on() {
     let mut console = BufferConsole::default();
diff --git a/crates/biome_cli/tests/snapshots/main_commands_lint/should_skip_nonexistent_changed_files.snap b/crates/biome_cli/tests/snapshots/main_commands_lint/should_skip_nonexistent_changed_files.snap
new file mode 100644
index 000000000000..68bcd4926ac9
--- /dev/null
+++ b/crates/biome_cli/tests/snapshots/main_commands_lint/should_skip_nonexistent_changed_files.snap
@@ -0,0 +1,15 @@
+---
+source: crates/biome_cli/tests/snap_test.rs
+expression: redactor(content)
+---
+## `exists.js`
+
+```js
+console.log('exists');
+```
+
+# Emitted Messages
+
+```block
+Checked 1 file in <TIME>. No fixes applied.
+```
diff --git a/crates/biome_cli/tests/snapshots/main_commands_lint/should_skip_nonexistent_staged_files.snap b/crates/biome_cli/tests/snapshots/main_commands_lint/should_skip_nonexistent_staged_files.snap
new file mode 100644
index 000000000000..68bcd4926ac9
--- /dev/null
+++ b/crates/biome_cli/tests/snapshots/main_commands_lint/should_skip_nonexistent_staged_files.snap
@@ -0,0 +1,15 @@
+---
+source: crates/biome_cli/tests/snap_test.rs
+expression: redactor(content)
+---
+## `exists.js`
+
+```js
+console.log('exists');
+```
+
+# Emitted Messages
+
+```block
+Checked 1 file in <TIME>. No fixes applied.
+```