diff --git a/src/whisper.cpp b/src/whisper.cpp
index 796bccfb45d..41a29e868ff 100644
--- a/src/whisper.cpp
+++ b/src/whisper.cpp
@@ -2317,7 +2317,11 @@ static struct ggml_cgraph * whisper_build_graph_cross(
         struct ggml_tensor * k;
         struct ggml_tensor * v;
 
-        if (wctx.params.flash_attn) {
+        // Use non-flash layout for cross-attention KV when DTW is enabled,
+        // since DTW needs the explicit cross-attention weights (KQ_soft_max)
+        const bool flash_cross = wctx.params.flash_attn && !wctx.params.dtw_token_timestamps;
+
+        if (flash_cross) {
             k = ggml_view_1d(ctx0, wstate.kv_cross.k, n_state*n_ctx,
                     (ggml_element_size(wstate.kv_cross.k)*n_state)*(il*n_ctx_pad));
 
@@ -2677,7 +2681,11 @@ static struct ggml_cgraph * whisper_build_graph_decoder(
                         ggml_reshape_3d(ctx0, Qcur, n_state_head, n_head, n_tokens),
                         0, 2, 1, 3);
 
-            if (wctx.params.flash_attn) {
+            // Use non-flash path for cross-attention when DTW is enabled,
+            // since DTW needs the explicit cross-attention weights (KQ_soft_max)
+            const bool flash_cross = wctx.params.flash_attn && !wctx.params.dtw_token_timestamps;
+
+            if (flash_cross) {
                 struct ggml_tensor * Kcross =
                     ggml_view_3d(ctx0, wstate.kv_cross.k,
                             n_state_head, n_audio_ctx_pad, n_head,
@@ -3706,8 +3714,7 @@ struct whisper_context * whisper_init_with_params_no_state(struct whisper_model_
     ggml_time_init();
 
     if (params.flash_attn && params.dtw_token_timestamps) {
-        WHISPER_LOG_WARN("%s: dtw_token_timestamps is not supported with flash_attn - disabling\n", __func__);
-        params.dtw_token_timestamps = false;
+        WHISPER_LOG_INFO("%s: flash_attn with dtw - disabling flash attention for cross-attention only\n", __func__);
     }
 
     WHISPER_LOG_INFO("%s: use gpu    = %d\n", __func__, params.use_gpu);