diff --git a/src/main/repository/NoteRepository.ts b/src/main/repository/NoteRepository.ts
index f980679..644d535 100644
--- a/src/main/repository/NoteRepository.ts
+++ b/src/main/repository/NoteRepository.ts
@@ -83,17 +83,25 @@ export class NoteRepository {
     const limit = Math.max(1, Math.min(200, opts.limit));
     const rows = opts.cursor
       ? (this.db
-          .prepare(`SELECT * FROM notes WHERE created_at < ? ORDER BY created_at DESC, id DESC LIMIT ?`)
+          .prepare(
+            `SELECT * FROM notes
+              WHERE deleted_at IS NULL AND created_at < ?
+              ORDER BY created_at DESC, id DESC LIMIT ?`
+          )
           .all(opts.cursor, limit) as any[])
       : (this.db
-          .prepare(`SELECT * FROM notes ORDER BY created_at DESC, id DESC LIMIT ?`)
+          .prepare(
+            `SELECT * FROM notes
+              WHERE deleted_at IS NULL
+              ORDER BY created_at DESC, id DESC LIMIT ?`
+          )
           .all(limit) as any[]);
     return rows.map((r) => this.hydrate(r));
   }
 
   listAll(): Note[] {
     const rows = this.db
-      .prepare(`SELECT * FROM notes ORDER BY created_at ASC, id ASC`)
+      .prepare(`SELECT * FROM notes WHERE deleted_at IS NULL ORDER BY created_at ASC, id ASC`)
       .all() as any[];
     return rows.map((r) => this.hydrate(r));
   }
@@ -359,7 +367,10 @@ export class NoteRepository {
     const startIso = new Date(kstMidnightUtc).toISOString();
     const endIso = new Date(nextKstMidnightUtc).toISOString();
     const row = this.db
-      .prepare(`SELECT COUNT(*) AS c FROM notes WHERE created_at >= ? AND created_at < ?`)
+      .prepare(
+        `SELECT COUNT(*) AS c FROM notes
+          WHERE deleted_at IS NULL AND created_at >= ? AND created_at < ?`
+      )
       .get(startIso, endIso) as { c: number };
     return row.c;
   }
diff --git a/tests/unit/NoteRepository.test.ts b/tests/unit/NoteRepository.test.ts
index 1099b55..578b318 100644
--- a/tests/unit/NoteRepository.test.ts
+++ b/tests/unit/NoteRepository.test.ts
@@ -363,3 +363,44 @@ describe('NoteRepository.listTrashed', () => {
     expect(r).toHaveLength(3);
   });
 });
+
+describe('Active queries exclude deleted notes', () => {
+  let db: Database.Database;
+  let repo: NoteRepository;
+  beforeEach(() => {
+    db = new Database(':memory:');
+    runMigrations(db);
+    repo = new NoteRepository(db);
+  });
+
+  it('list() excludes trashed', () => {
+    const a = repo.create({ rawText: 'a' }).id;
+    const b = repo.create({ rawText: 'b' }).id;
+    repo.trash(a, '2026-05-01T00:00:00.000Z');
+    const r = repo.list({ limit: 50 });
+    expect(r.map((n) => n.id)).toEqual([b]);
+  });
+
+  it('listAll() excludes trashed', () => {
+    const a = repo.create({ rawText: 'a' }).id;
+    repo.create({ rawText: 'b' });
+    repo.trash(a, '2026-05-01T00:00:00.000Z');
+    const r = repo.listAll();
+    expect(r.map((n) => n.rawText)).toEqual(['b']);
+  });
+
+  it('countToday() excludes trashed', () => {
+    const a = repo.create({ rawText: 'a' }).id;
+    repo.create({ rawText: 'b' });
+    repo.trash(a, new Date().toISOString());
+    expect(repo.countToday(new Date())).toBe(1);
+  });
+
+  it('findById() returns trashed notes (does NOT filter)', () => {
+    const { id } = repo.create({ rawText: 'a' });
+    repo.trash(id, '2026-05-01T00:00:00.000Z');
+    const note = repo.findById(id);
+    expect(note).not.toBeNull();
+    expect(note!.deletedAt).toBe('2026-05-01T00:00:00.000Z');
+  });
+});