diff --git a/src/aci/cli/__init__.py b/src/aci/cli/__init__.py
index efb018d..cd3ded7 100644
--- a/src/aci/cli/__init__.py
+++ b/src/aci/cli/__init__.py
@@ -22,7 +22,11 @@
 from rich.syntax import Syntax
 from rich.table import Table
 
-from aci.core.path_utils import get_collection_name_for_path, validate_indexable_path
+from aci.core.path_utils import (
+    get_collection_name_for_path,
+    resolve_file_filter_pattern,
+    validate_indexable_path,
+)
 from aci.infrastructure import GrepSearcher
 from aci.infrastructure.codebase_registry import (
     CodebaseRegistryStore,
@@ -236,6 +240,7 @@ def search(
             console.print(f"[bold red]Error:[/bold red] {resolution.error_message}")
             raise typer.Exit(1)
         collection_name = resolution.collection_name
+        normalized_file_filter = resolve_file_filter_pattern(file_filter, resolution.indexed_root)
 
         # Use config values if not overridden by CLI
         actual_limit = limit if limit is not None else cfg.search.default_limit
@@ -291,7 +296,7 @@ def search(
                 search_service.search(
                     query=query,
                     limit=actual_limit,
-                    file_filter=file_filter,  # User-provided filter only
+                    file_filter=normalized_file_filter,
                     use_rerank=use_rerank and reranker is not None,
                     search_mode=search_mode,  # Pass search mode
                     collection_name=collection_name,  # Pass explicitly, no state mutation
diff --git a/src/aci/core/path_utils.py b/src/aci/core/path_utils.py
index a1ad9ac..bcbc8b4 100644
--- a/src/aci/core/path_utils.py
+++ b/src/aci/core/path_utils.py
@@ -173,6 +173,41 @@ def parse_runtime_path_mappings(raw_value: str | None) -> list[RuntimePathMappin
     return mappings
 
 
+def resolve_file_filter_pattern(
+    file_filter: str | None, indexed_root: str | Path | None
+) -> str | None:
+    """Resolve relative file-filter prefixes against the indexed root path.
+
+    Keeps broad wildcard-only patterns unchanged (e.g. ``*.py`` or ``**/*.py``),
+    but expands relative directory-prefixed patterns (e.g. ``src/**/*.py``)
+    to absolute patterns rooted at ``indexed_root``.
+    """
+    if not file_filter:
+        return file_filter
+    if indexed_root is None:
+        return file_filter
+
+    raw_filter = file_filter.strip()
+    if not raw_filter:
+        return raw_filter
+
+    # Already absolute (POSIX, Windows drive, or UNC path).
+    if raw_filter.startswith("/") or _looks_like_windows_path(raw_filter) or raw_filter.startswith("\\\\"):
+        return raw_filter
+
+    normalized = raw_filter.replace("\\", "/")
+    has_directory_prefix = "/" in normalized
+    starts_with_wildcard = normalized.startswith(("*", "?", "["))
+    if not has_directory_prefix or starts_with_wildcard:
+        return raw_filter
+
+    relative_filter = normalized.lstrip("./")
+    if not relative_filter:
+        return raw_filter
+
+    return str(Path(indexed_root).resolve() / Path(relative_filter))
+
+
 def _apply_runtime_path_mapping(
     path_str: str,
     path_mappings: Sequence[RuntimePathMapping],
diff --git a/src/aci/http_server.py b/src/aci/http_server.py
index e17cb9e..51bead8 100644
--- a/src/aci/http_server.py
+++ b/src/aci/http_server.py
@@ -11,7 +11,11 @@
 from fastapi import FastAPI, HTTPException, Query
 from pydantic import BaseModel
 
-from aci.core.path_utils import get_collection_name_for_path, is_system_directory
+from aci.core.path_utils import (
+    get_collection_name_for_path,
+    is_system_directory,
+    resolve_file_filter_pattern,
+)
 from aci.core.watch_config import WatchConfig
 from aci.infrastructure.codebase_registry import best_effort_update_registry
 from aci.infrastructure.file_watcher import FileWatcher
@@ -330,6 +334,7 @@ async def search(
                 raise HTTPException(status_code=400, detail=resolution.error_message)
 
             collection_name = resolution.collection_name
+            normalized_file_filter = resolve_file_filter_pattern(file_filter, resolution.indexed_root)
 
             apply_rerank = cfg.search.use_rerank if use_rerank is None else use_rerank
 
@@ -363,7 +368,7 @@ async def search(
             results = await search_service.search(
                 query=q,
                 limit=limit,
-                file_filter=file_filter,
+                file_filter=normalized_file_filter,
                 use_rerank=apply_rerank,
                 search_mode=search_mode,
                 collection_name=collection_name,
diff --git a/src/aci/mcp/handlers.py b/src/aci/mcp/handlers.py
index 3f3981d..324fed8 100644
--- a/src/aci/mcp/handlers.py
+++ b/src/aci/mcp/handlers.py
@@ -11,6 +11,7 @@
 from aci.core.path_utils import (
     RuntimePathResolutionResult,
     get_collection_name_for_path,
+    resolve_file_filter_pattern,
     resolve_runtime_path,
     validate_indexable_path,
 )
@@ -243,6 +244,8 @@ async def _handle_search_code(arguments: dict, ctx: MCPContext) -> list[TextCont
                      f"Valid types: {', '.join(sorted(valid_artifact_types))}"
             )]
 
+    normalized_file_filter = resolve_file_filter_pattern(file_filter, indexed_root)
+
     # Request more results if filtering by subdirectory (to ensure enough after filtering)
     fetch_limit = limit * 3 if path_prefix_filter else limit
 
@@ -250,7 +253,7 @@ async def _handle_search_code(arguments: dict, ctx: MCPContext) -> list[TextCont
     results = await search_service.search(
         query=query,
         limit=fetch_limit,
-        file_filter=file_filter,
+        file_filter=normalized_file_filter,
         use_rerank=use_rerank,
         search_mode=search_mode,
         collection_name=collection_name,
diff --git a/tests/unit/test_runtime_path_resolution.py b/tests/unit/test_runtime_path_resolution.py
index 2749f0b..60a1f13 100644
--- a/tests/unit/test_runtime_path_resolution.py
+++ b/tests/unit/test_runtime_path_resolution.py
@@ -107,3 +107,28 @@ def test_mcp_index_codebase_uses_resolved_runtime_path(tmp_path: Path):
     payload = json.loads(result[0].text)
     assert payload["requested_path"] == r"D:\workspace"
     assert payload["indexed_path"] == str(mounted_repo.resolve())
+
+
+def test_resolve_file_filter_pattern_keeps_wildcard_only_pattern(tmp_path: Path):
+    from aci.core.path_utils import resolve_file_filter_pattern
+
+    resolved = resolve_file_filter_pattern("**/*.tsx", tmp_path)
+
+    assert resolved == "**/*.tsx"
+
+
+def test_resolve_file_filter_pattern_expands_relative_prefixed_pattern(tmp_path: Path):
+    from aci.core.path_utils import resolve_file_filter_pattern
+
+    resolved = resolve_file_filter_pattern("apps/web/**/*.tsx", tmp_path)
+
+    assert resolved == str(tmp_path.resolve() / "apps/web/**/*.tsx")
+
+
+def test_resolve_file_filter_pattern_keeps_absolute_pattern(tmp_path: Path):
+    from aci.core.path_utils import resolve_file_filter_pattern
+
+    absolute_pattern = str(tmp_path / "apps/**/*.tsx")
+    resolved = resolve_file_filter_pattern(absolute_pattern, "/another/root")
+
+    assert resolved == absolute_pattern