diff --git a/src/cli/cli.c b/src/cli/cli.c
index bc2d13189..08b1be678 100644
--- a/src/cli/cli.c
+++ b/src/cli/cli.c
@@ -2860,6 +2860,9 @@ int cbm_config_delete(cbm_config_t *cfg, const char *key) {
 
 /* ── Config registry ──────────────────────────────────────────── */
 
+/* Hand-wrapped for readable help text; automatic formatting makes this table
+ * substantially narrower and churns unrelated entries. */
+// clang-format off
 const cbm_config_entry_t CBM_CONFIG_REGISTRY[] = {
     /* ── Indexing ── */
     {"auto_index", "true", "CBM_AUTO_INDEX", "Indexing",
@@ -2871,6 +2874,10 @@ const cbm_config_entry_t CBM_CONFIG_REGISTRY[] = {
      "0-10000000",
      "Protects against accidentally indexing huge monorepos. Raise for large codebases. "
      "Set 0 to disable the limit and always index regardless of repo size."},
+    {CBM_CONFIG_EXTRACT_TIMEOUT_MS, CBM_CONFIG_EXTRACT_TIMEOUT_DEFAULT, NULL, "Indexing",
+     "Per-file tree-sitter parse deadline in milliseconds",
+     "100-120000",
+     "Bounds pathological parses. A timeout fails the indexing transaction and preserves the prior database; raise only for measured large-file workloads or instrumented tests."},
     {"reindex_on_startup", "false", "CBM_REINDEX_ON_STARTUP", "Indexing",
      "Re-index stale projects when server starts",
      "true|false",
@@ -3225,6 +3232,7 @@ const cbm_config_entry_t CBM_CONFIG_REGISTRY[] = {
      "Set 0 for unlimited if you need complete large-package analysis."},
     {NULL, NULL, NULL, NULL, NULL, NULL, NULL} /* sentinel */
 };
+// clang-format on
 
 /* Get config value with env var override priority: env > db > default.
  * Looks up the registry entry for the key to find the env var name. */
diff --git a/src/pipeline/pass_calls.c b/src/pipeline/pass_calls.c
index 1bbc107e0..0fd3e879a 100644
--- a/src/pipeline/pass_calls.c
+++ b/src/pipeline/pass_calls.c
@@ -410,9 +410,10 @@ static CBMFileResult *calls_get_or_extract(cbm_pipeline_ctx_t *ctx, int idx,
     if (!src) {
         return NULL;
     }
-    CBMFileResult *r = cbm_extract_file_with_options(
-        src, slen, fi->language, ctx->project_name, fi->rel_path, CBM_EXTRACT_BUDGET, NULL, NULL,
-        cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
+    CBMFileResult *r =
+        cbm_extract_file_with_options(src, slen, fi->language, ctx->project_name, fi->rel_path,
+                                      cbm_pipeline_ctx_extract_timeout(ctx), NULL, NULL,
+                                      cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
     free(src);
     if (r) {
         *owned = true;
diff --git a/src/pipeline/pass_definitions.c b/src/pipeline/pass_definitions.c
index 0b27e195b..a33d043c6 100644
--- a/src/pipeline/pass_definitions.c
+++ b/src/pipeline/pass_definitions.c
@@ -462,8 +462,8 @@ int cbm_pipeline_pass_definitions(cbm_pipeline_ctx_t *ctx, const cbm_file_info_t
 
         /* Extract */
         CBMFileResult *result = cbm_extract_file_with_options(
-            source, source_len, lang, ctx->project_name, rel, CBM_EXTRACT_BUDGET, NULL,
-            NULL /* no extra defines or include paths */,
+            source, source_len, lang, ctx->project_name, rel, cbm_pipeline_ctx_extract_timeout(ctx),
+            NULL, NULL /* no extra defines or include paths */,
             cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
         free(source);
 
diff --git a/src/pipeline/pass_k8s.c b/src/pipeline/pass_k8s.c
index 4d48cb7e3..8ef3609a4 100644
--- a/src/pipeline/pass_k8s.c
+++ b/src/pipeline/pass_k8s.c
@@ -108,10 +108,10 @@ static void handle_kustomize(cbm_pipeline_ctx_t *ctx, const char *path, const ch
         int src_len = 0;
         char *source = k8s_read_file(path, &src_len);
         if (source) {
-            res = cbm_extract_file_with_options(
-                source, src_len, CBM_LANG_KUSTOMIZE, ctx->project_name, rel_path,
-                CBM_EXTRACT_BUDGET, NULL, NULL,
-                cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
+            res = cbm_extract_file_with_options(source, src_len, CBM_LANG_KUSTOMIZE,
+                                                ctx->project_name, rel_path,
+                                                cbm_pipeline_ctx_extract_timeout(ctx), NULL, NULL,
+                                                cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
             free(source);
             allocated = true;
         }
@@ -377,9 +377,10 @@ static void handle_k8s_manifest(cbm_pipeline_ctx_t *ctx, const char *path, const
     (void)path; /* retained for symmetry; source is always provided now */
     int resource_count = 0;
 
-    CBMFileResult *res = cbm_extract_file_with_options(
-        source, src_len, CBM_LANG_K8S, ctx->project_name, rel_path, CBM_EXTRACT_BUDGET, NULL, NULL,
-        cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
+    CBMFileResult *res =
+        cbm_extract_file_with_options(source, src_len, CBM_LANG_K8S, ctx->project_name, rel_path,
+                                      cbm_pipeline_ctx_extract_timeout(ctx), NULL, NULL,
+                                      cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
     if (!res) {
         return;
     }
diff --git a/src/pipeline/pass_parallel.c b/src/pipeline/pass_parallel.c
index bb4f5436f..c3b64b02e 100644
--- a/src/pipeline/pass_parallel.c
+++ b/src/pipeline/pass_parallel.c
@@ -421,6 +421,7 @@ typedef struct {
     cbm_pkg_entries_t *pkg_entries; /* per-worker manifest arrays (separate allocation) */
     _Atomic int64_t retained_bytes; /* total source bytes copied into result arenas */
     bool extract_macros;
+    int64_t extract_timeout_micros;
 } extract_ctx_t;
 
 /* Insert one definition node (and its route if present) into the local gbuf. */
@@ -524,8 +525,8 @@ static void extract_worker(int worker_id, void *ctx_ptr) {
         uint64_t file_t0 = extract_now_ns();
 
         CBMFileResult *result = cbm_extract_file_with_options(
-            source, source_len, fi->language, ec->project_name, fi->rel_path, CBM_EXTRACT_BUDGET,
-            NULL, NULL, ec->extract_macros);
+            source, source_len, fi->language, ec->project_name, fi->rel_path,
+            ec->extract_timeout_micros, NULL, NULL, ec->extract_macros);
 
         uint64_t file_elapsed_ms = (extract_now_ns() - file_t0) / PP_USEC_PER_MS;
 
@@ -717,6 +718,7 @@ int cbm_parallel_extract(cbm_pipeline_ctx_t *ctx, const cbm_file_info_t *files,
         .cancelled = ctx->cancelled,
         .pkg_entries = pkg_entries,
         .extract_macros = cbm_pipeline_mode_extracts_macro_nodes(ctx->mode),
+        .extract_timeout_micros = cbm_pipeline_ctx_extract_timeout(ctx),
     };
     atomic_init(&ec.next_worker_id, 0);
     atomic_init(&ec.next_file_idx, 0);
diff --git a/src/pipeline/pass_semantic.c b/src/pipeline/pass_semantic.c
index 263092fbb..a045e1ed8 100644
--- a/src/pipeline/pass_semantic.c
+++ b/src/pipeline/pass_semantic.c
@@ -381,9 +381,10 @@ static CBMFileResult *sem_get_or_extract(cbm_pipeline_ctx_t *ctx, int file_idx,
     if (!source) {
         return NULL;
     }
-    CBMFileResult *r = cbm_extract_file_with_options(
-        source, source_len, fi->language, ctx->project_name, fi->rel_path, CBM_EXTRACT_BUDGET,
-        NULL, NULL, cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
+    CBMFileResult *r =
+        cbm_extract_file_with_options(source, source_len, fi->language, ctx->project_name,
+                                      fi->rel_path, cbm_pipeline_ctx_extract_timeout(ctx), NULL,
+                                      NULL, cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
     free(source);
     if (r) {
         *owned = true;
diff --git a/src/pipeline/pass_usages.c b/src/pipeline/pass_usages.c
index 64bc7eb78..ba2057cfa 100644
--- a/src/pipeline/pass_usages.c
+++ b/src/pipeline/pass_usages.c
@@ -232,8 +232,9 @@ int cbm_pipeline_pass_usages(cbm_pipeline_ctx_t *ctx, const cbm_file_info_t *fil
                 continue;
             }
             result = cbm_extract_file_with_options(
-                source, source_len, files[i].language, ctx->project_name, rel, CBM_EXTRACT_BUDGET,
-                NULL, NULL, cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
+                source, source_len, files[i].language, ctx->project_name, rel,
+                cbm_pipeline_ctx_extract_timeout(ctx), NULL, NULL,
+                cbm_pipeline_mode_extracts_macro_nodes(ctx->mode));
             free(source);
             if (!result) {
                 errors++;
diff --git a/src/pipeline/pipeline.c b/src/pipeline/pipeline.c
index be47c470b..b2abf9a88 100644
--- a/src/pipeline/pipeline.c
+++ b/src/pipeline/pipeline.c
@@ -112,6 +112,7 @@ struct cbm_pipeline {
     double semantic_threshold;
     double githistory_min_coupling;
     double lsp_confidence_floor;
+    int64_t extract_timeout_micros;
     cbm_incremental_reindex_policy_t incremental_reindex;
     cbm_overlay_publish_policy_t overlay_publish;
     cbm_incremental_derived_refresh_policy_t incremental_derived_refresh;
@@ -205,6 +206,7 @@ cbm_pipeline_t *cbm_pipeline_new(const char *repo_path, const char *db_path,
     p->semantic_threshold = 0.0;
     p->githistory_min_coupling = 0.0;
     p->lsp_confidence_floor = 0.0;
+    p->extract_timeout_micros = CBM_EXTRACT_BUDGET;
     p->incremental_reindex = CBM_INCREMENTAL_REINDEX_OFF;
     p->overlay_publish = CBM_OVERLAY_PUBLISH_OFF;
     p->incremental_derived_refresh = CBM_INCREMENTAL_DERIVED_REFRESH_STALE_ON_INCREMENTAL;
@@ -346,6 +348,15 @@ void cbm_pipeline_apply_config(cbm_pipeline_t *p, cbm_config_t *cfg) {
         cbm_pipeline_set_lsp_confidence_floor(p, lsp_floor);
     }
 
+    int extract_timeout_ms = cbm_config_get_int(cfg, CBM_CONFIG_EXTRACT_TIMEOUT_MS,
+                                                CBM_CONFIG_EXTRACT_TIMEOUT_DEFAULT_MS);
+    if (extract_timeout_ms < CBM_CONFIG_EXTRACT_TIMEOUT_MIN_MS) {
+        extract_timeout_ms = CBM_CONFIG_EXTRACT_TIMEOUT_MIN_MS;
+    } else if (extract_timeout_ms > CBM_CONFIG_EXTRACT_TIMEOUT_MAX_MS) {
+        extract_timeout_ms = CBM_CONFIG_EXTRACT_TIMEOUT_MAX_MS;
+    }
+    p->extract_timeout_micros = (int64_t)extract_timeout_ms * 1000;
+
     const char *incremental =
         cbm_config_get(cfg, CBM_CONFIG_INCREMENTAL_REINDEX, CBM_CONFIG_INCREMENTAL_REINDEX_OFF);
     if (incremental && strcmp(incremental, CBM_CONFIG_INCREMENTAL_REINDEX_ALWAYS) == 0) {
@@ -405,6 +416,10 @@ double cbm_pipeline_lsp_confidence_floor(const cbm_pipeline_t *p) {
     return p ? p->lsp_confidence_floor : 0.0;
 }
 
+int64_t cbm_pipeline_extract_timeout_micros(const cbm_pipeline_t *p) {
+    return p ? p->extract_timeout_micros : CBM_EXTRACT_BUDGET;
+}
+
 int cbm_pipeline_exact_max_changed_paths(const cbm_pipeline_t *p) {
     return p ? p->exact_delta_max_changed_paths
              : CBM_PIPELINE_EXACT_DELTA_DEFAULT_MAX_CHANGED_PATHS;
@@ -1765,6 +1780,7 @@ int cbm_pipeline_run(cbm_pipeline_t *p) {
         .semantic_threshold = p->semantic_threshold,
         .githistory_min_coupling = p->githistory_min_coupling,
         .lsp_confidence_floor = p->lsp_confidence_floor,
+        .extract_timeout_micros = p->extract_timeout_micros,
         .path_aliases = path_aliases,
     };
 
diff --git a/src/pipeline/pipeline.h b/src/pipeline/pipeline.h
index 98fdc946a..72871b4d2 100644
--- a/src/pipeline/pipeline.h
+++ b/src/pipeline/pipeline.h
@@ -105,6 +105,11 @@ void cbm_pipeline_set_flush_store(cbm_pipeline_t *p, cbm_store_t *store);
 #define CBM_CONFIG_SEMANTIC_THRESHOLD "semantic_threshold"
 #define CBM_CONFIG_GITHISTORY_MIN_COUPLING "githistory_min_coupling"
 #define CBM_CONFIG_LSP_CONFIDENCE_FLOOR "lsp_confidence_floor"
+#define CBM_CONFIG_EXTRACT_TIMEOUT_MS "extract_timeout_ms"
+#define CBM_CONFIG_EXTRACT_TIMEOUT_DEFAULT_MS 5000
+#define CBM_CONFIG_EXTRACT_TIMEOUT_DEFAULT "5000"
+#define CBM_CONFIG_EXTRACT_TIMEOUT_MIN_MS 100
+#define CBM_CONFIG_EXTRACT_TIMEOUT_MAX_MS 120000
 #define CBM_CONFIG_INCREMENTAL_REINDEX "incremental_reindex"
 #define CBM_CONFIG_INCREMENTAL_REINDEX_OFF "off"
 #define CBM_CONFIG_INCREMENTAL_REINDEX_FAST "fast"
diff --git a/src/pipeline/pipeline_incremental.c b/src/pipeline/pipeline_incremental.c
index c83f4b56d..51c212ac7 100644
--- a/src/pipeline/pipeline_incremental.c
+++ b/src/pipeline/pipeline_incremental.c
@@ -1732,6 +1732,7 @@ static int incr_try_overlay_upsert_route(cbm_pipeline_t *p, cbm_store_t *store,
         .semantic_threshold = cbm_pipeline_semantic_threshold(p),
         .githistory_min_coupling = cbm_pipeline_githistory_min_coupling(p),
         .lsp_confidence_floor = cbm_pipeline_lsp_confidence_floor(p),
+        .extract_timeout_micros = cbm_pipeline_extract_timeout_micros(p),
         .path_aliases = path_aliases,
         .pkgmap_preseeded = true,
         .result_cache = result_cache,
@@ -2096,6 +2097,7 @@ static int incr_try_exact_upsert_route(cbm_pipeline_t *p, cbm_store_t *store, co
         .semantic_threshold = cbm_pipeline_semantic_threshold(p),
         .githistory_min_coupling = cbm_pipeline_githistory_min_coupling(p),
         .lsp_confidence_floor = cbm_pipeline_lsp_confidence_floor(p),
+        .extract_timeout_micros = cbm_pipeline_extract_timeout_micros(p),
         .path_aliases = path_aliases,
         .pkgmap_preseeded = true,
         .result_cache = result_cache,
@@ -2751,6 +2753,7 @@ int cbm_pipeline_run_incremental(cbm_pipeline_t *p, const char *db_path, cbm_fil
         .semantic_threshold = cbm_pipeline_semantic_threshold(p),
         .githistory_min_coupling = cbm_pipeline_githistory_min_coupling(p),
         .lsp_confidence_floor = cbm_pipeline_lsp_confidence_floor(p),
+        .extract_timeout_micros = cbm_pipeline_extract_timeout_micros(p),
         .path_aliases = path_aliases,
     };
 
diff --git a/src/pipeline/pipeline_internal.h b/src/pipeline/pipeline_internal.h
index 775ef6ef1..c177824d6 100644
--- a/src/pipeline/pipeline_internal.h
+++ b/src/pipeline/pipeline_internal.h
@@ -404,6 +404,7 @@ typedef struct {
     double semantic_threshold;         /* <=0 uses semantic default 0.75 */
     double githistory_min_coupling;    /* <=0 uses git-history default 0.3 */
     double lsp_confidence_floor;       /* <=0 uses LSP default 0.6 */
+    int64_t extract_timeout_micros;    /* bounded tree-sitter parse deadline */
 
     /* Extraction result cache (sequential pipeline optimization).
      * When non-NULL, pass_definitions stores results here instead of freeing,
@@ -437,6 +438,13 @@ typedef struct {
     int store_backed_lsp_scope_cap;
 } cbm_pipeline_ctx_t;
 
+static inline int64_t cbm_pipeline_ctx_extract_timeout(const cbm_pipeline_ctx_t *ctx) {
+    return ctx && ctx->extract_timeout_micros > 0 ? ctx->extract_timeout_micros
+                                                  : CBM_EXTRACT_BUDGET;
+}
+
+int64_t cbm_pipeline_extract_timeout_micros(const cbm_pipeline_t *p);
+
 static inline bool cbm_pipeline_mode_builds_global_semantic_edges(int mode) {
     return mode == CBM_MODE_FULL || mode == CBM_MODE_MODERATE;
 }
diff --git a/tests/test_incremental.c b/tests/test_incremental.c
index a3ada7771..550e964ac 100644
--- a/tests/test_incremental.c
+++ b/tests/test_incremental.c
@@ -60,6 +60,7 @@ enum {
     INCR_ACCURACY_EDGE_TOLERANCE = 50,
     INCR_ACCURACY_CALL_TOLERANCE = 2,
     INCR_FULL_INDEX_MAX_RSS_DELTA_MB = 2048,
+    INCR_INSTRUMENTED_TIMEOUT_MULTIPLIER = 4,
 };
 
 static const char *INCR_TEST_ARTIFACT_ENV = "CBM_TEST_ARTIFACT_DIR";
@@ -592,6 +593,12 @@ static int incremental_setup(void) {
         return -1;
     }
     cbm_config_set(g_cfg, CBM_CONFIG_INCREMENTAL_REINDEX, "always");
+    if (incr_memory_instrumentation_active()) {
+        char timeout_ms[CBM_SZ_32];
+        snprintf(timeout_ms, sizeof(timeout_ms), "%d",
+                 CBM_CONFIG_EXTRACT_TIMEOUT_DEFAULT_MS * INCR_INSTRUMENTED_TIMEOUT_MULTIPLIER);
+        cbm_config_set(g_cfg, CBM_CONFIG_EXTRACT_TIMEOUT_MS, timeout_ms);
+    }
     cbm_mcp_server_set_config(g_srv, g_cfg);
 
     g_rss_before_full = cbm_mem_rss();
diff --git a/tests/test_pipeline.c b/tests/test_pipeline.c
index abcf52d5a..0c4c189d7 100644
--- a/tests/test_pipeline.c
+++ b/tests/test_pipeline.c
@@ -14608,6 +14608,7 @@ TEST(pipeline_apply_config_sets_all_thresholds) {
     ASSERT_EQ(cbm_config_set(cfg, CBM_CONFIG_SEMANTIC_THRESHOLD, "0.76"), 0);
     ASSERT_EQ(cbm_config_set(cfg, CBM_CONFIG_GITHISTORY_MIN_COUPLING, "0.31"), 0);
     ASSERT_EQ(cbm_config_set(cfg, CBM_CONFIG_LSP_CONFIDENCE_FLOOR, "0.61"), 0);
+    ASSERT_EQ(cbm_config_set(cfg, CBM_CONFIG_EXTRACT_TIMEOUT_MS, "17000"), 0);
     char max_changed[CBM_SZ_32];
     char max_affected[CBM_SZ_32];
     int n = snprintf(max_changed, sizeof(max_changed), "%d", PIPELINE_TEST_EXACT_MAX_CHANGED);
@@ -14633,11 +14634,21 @@ TEST(pipeline_apply_config_sets_all_thresholds) {
     ASSERT_TRUE(cbm_pipeline_githistory_min_coupling(p) < 0.32);
     ASSERT_TRUE(cbm_pipeline_lsp_confidence_floor(p) > 0.60);
     ASSERT_TRUE(cbm_pipeline_lsp_confidence_floor(p) < 0.62);
+    ASSERT_EQ(cbm_pipeline_extract_timeout_micros(p), 17000000);
     ASSERT_EQ(cbm_pipeline_exact_max_changed_paths(p), PIPELINE_TEST_EXACT_MAX_CHANGED);
     ASSERT_EQ(cbm_pipeline_exact_max_affected_paths(p), PIPELINE_TEST_EXACT_MAX_AFFECTED);
     ASSERT_TRUE(cbm_pipeline_incremental_derived_refresh_stale_on_exact(p));
     ASSERT_TRUE(cbm_pipeline_incremental_derived_refresh_stale_on_incremental(p));
 
+    ASSERT_EQ(cbm_config_set(cfg, CBM_CONFIG_EXTRACT_TIMEOUT_MS, "1"), 0);
+    cbm_pipeline_apply_config(p, cfg);
+    ASSERT_EQ(cbm_pipeline_extract_timeout_micros(p),
+              (int64_t)CBM_CONFIG_EXTRACT_TIMEOUT_MIN_MS * 1000);
+    ASSERT_EQ(cbm_config_set(cfg, CBM_CONFIG_EXTRACT_TIMEOUT_MS, "999999"), 0);
+    cbm_pipeline_apply_config(p, cfg);
+    ASSERT_EQ(cbm_pipeline_extract_timeout_micros(p),
+              (int64_t)CBM_CONFIG_EXTRACT_TIMEOUT_MAX_MS * 1000);
+
     cbm_pipeline_free(p);
     cbm_config_close(cfg);
     rm_rf(tmpdir);
@@ -14900,6 +14911,15 @@ TEST(config_registry_includes_incremental_reindex_policy) {
     PASS();
 }
 
+TEST(config_registry_includes_extract_timeout) {
+    const cbm_config_entry_t *entry = find_config_entry(CBM_CONFIG_EXTRACT_TIMEOUT_MS);
+    ASSERT_NOT_NULL(entry);
+    ASSERT_STR_EQ(entry->default_val, CBM_CONFIG_EXTRACT_TIMEOUT_DEFAULT);
+    ASSERT_STR_EQ(entry->category, "Indexing");
+    ASSERT_STR_EQ(entry->range, "100-120000");
+    PASS();
+}
+
 TEST(config_registry_includes_overlay_publish_policy) {
     const cbm_config_entry_t *entry = find_config_entry(CBM_CONFIG_OVERLAY_PUBLISH);
     ASSERT_NOT_NULL(entry);
@@ -15670,6 +15690,7 @@ SUITE(pipeline) {
     RUN_TEST(pipeline_semantic_batch_rejects_invalid_token_stride);
     RUN_TEST(config_registry_includes_mcp_timeout_knobs);
     RUN_TEST(config_registry_includes_incremental_reindex_policy);
+    RUN_TEST(config_registry_includes_extract_timeout);
     RUN_TEST(config_registry_includes_overlay_publish_policy);
     RUN_TEST(config_registry_includes_overlay_compaction_policy);
     RUN_TEST(config_registry_includes_incremental_exact_frontier_caps);