diff --git a/.changeset/violet-lions-travel.md b/.changeset/violet-lions-travel.md
new file mode 100644
index 000000000000..0236391d823c
--- /dev/null
+++ b/.changeset/violet-lions-travel.md
@@ -0,0 +1,5 @@
+---
+"@biomejs/biome": patch
+---
+
+Fixed [#9258](https://github.com/biomejs/biome/issues/9258): `--skip` no longer causes `suppressions/unused` warnings for suppression comments targeting skipped rules or domains.
diff --git a/crates/biome_cli/tests/cases/linter_domains.rs b/crates/biome_cli/tests/cases/linter_domains.rs
index 96b51d49b987..2c7392f27800 100644
--- a/crates/biome_cli/tests/cases/linter_domains.rs
+++ b/crates/biome_cli/tests/cases/linter_domains.rs
@@ -454,6 +454,52 @@ describe("foo", () => {
     ));
 }
 
+/// Regression test for https://github.com/biomejs/biome/issues/9258
+/// Skipping a domain should not report suppression comments for rules in that
+/// domain as unused.
+#[test]
+fn skip_domain_does_not_report_unused_suppression() {
+    let mut console = BufferConsole::default();
+    let fs = MemoryFileSystem::default();
+    let config = Utf8Path::new("biome.json");
+    fs.insert(
+        config.into(),
+        r#"{
+    "linter": {
+        "domains": {
+            "test": "all"
+        }
+    }
+}
+"#
+        .as_bytes(),
+    );
+    let test1 = Utf8Path::new("test1.js");
+    fs.insert(
+        test1.into(),
+        r#"// biome-ignore lint/suspicious/noFocusedTests: reason
+describe.only("bar", () => {});
+"#
+        .as_bytes(),
+    );
+
+    let (fs, result) = run_cli(
+        fs,
+        &mut console,
+        Args::from(["check", "--skip=test", test1.as_str()].as_slice()),
+    );
+
+    assert!(result.is_ok(), "run_cli returned {result:?}");
+
+    assert_cli_snapshot(SnapshotPayload::new(
+        module_path!(),
+        "skip_domain_does_not_report_unused_suppression",
+        fs,
+        console,
+        result,
+    ));
+}
+
 /// Verifies that explicit domain enables are additive with whole-group enables:
 /// the plain group contributes only non-domain rules, and the domain adds its
 /// domain-tagged rules back explicitly.
diff --git a/crates/biome_cli/tests/snapshots/main_cases_linter_domains/skip_domain_does_not_report_unused_suppression.snap b/crates/biome_cli/tests/snapshots/main_cases_linter_domains/skip_domain_does_not_report_unused_suppression.snap
new file mode 100644
index 000000000000..dacfd410407d
--- /dev/null
+++ b/crates/biome_cli/tests/snapshots/main_cases_linter_domains/skip_domain_does_not_report_unused_suppression.snap
@@ -0,0 +1,29 @@
+---
+source: crates/biome_cli/tests/snap_test.rs
+expression: redactor(content)
+---
+## `biome.json`
+
+```json
+{
+  "linter": {
+    "domains": {
+      "test": "all"
+    }
+  }
+}
+```
+
+## `test1.js`
+
+```js
+// biome-ignore lint/suspicious/noFocusedTests: reason
+describe.only("bar", () => {});
+
+```
+
+# Emitted Messages
+
+```block
+Checked 1 file in <TIME>. No fixes applied.
+```
diff --git a/crates/biome_service/src/file_handlers/mod.rs b/crates/biome_service/src/file_handlers/mod.rs
index f7c4efb75972..ad69deaafad7 100644
--- a/crates/biome_service/src/file_handlers/mod.rs
+++ b/crates/biome_service/src/file_handlers/mod.rs
@@ -641,9 +641,11 @@ impl<'a> ProcessLint<'a> {
             diagnostics: Default::default(),
             // Do not report unused suppression comment diagnostics if:
             // - it is a syntax-only analyzer pass, or
-            // - if a single rule is run.
+            // - if a single rule is run, or
+            // - if rules or domains are skipped.
             ignores_suppression_comment: !params.categories.contains(RuleCategory::Lint)
-                || !params.only.is_empty(),
+                || !params.only.is_empty()
+                || !params.skip.is_empty(),
             rules: params
                 .settings
                 .as_ref()