diff --git a/packages/transformers/src/models/whisper/modeling_whisper.js b/packages/transformers/src/models/whisper/modeling_whisper.js
index dfca02672..75c14bceb 100644
--- a/packages/transformers/src/models/whisper/modeling_whisper.js
+++ b/packages/transformers/src/models/whisper/modeling_whisper.js
@@ -116,7 +116,13 @@ export class WhisperForConditionalGeneration extends WhisperPreTrainedModel {
     }) {
         generation_config = this._prepare_generation_config(generation_config, kwargs);
 
-        const init_tokens = kwargs.decoder_input_ids ?? this._retrieve_init_tokens(generation_config);
+        let init_tokens = kwargs.decoder_input_ids ?? this._retrieve_init_tokens(generation_config);
+
+        // Prepend prompt_ids to init_tokens if provided (matches Whisper training format):
+        // [<|startofprev|>, ...prompt_text..., <|startoftranscript|>, <|lang|>, <|task|>, ...]
+        if (generation_config.prompt_ids) {
+            init_tokens = [...generation_config.prompt_ids, ...init_tokens];
+        }
 
         if (generation_config.return_timestamps) {
             logits_processor ??= new LogitsProcessorList();
@@ -146,7 +152,7 @@ export class WhisperForConditionalGeneration extends WhisperPreTrainedModel {
             generation_config.return_dict_in_generate = true;
         }
 
-        const outputs = await super.generate({
+        let outputs = await super.generate({
             inputs,
             generation_config,
             logits_processor,
@@ -154,6 +160,19 @@ export class WhisperForConditionalGeneration extends WhisperPreTrainedModel {
             ...kwargs,
         });
 
+        // Strip prompt_ids from output sequences so they don't appear in transcription
+        if (generation_config.prompt_ids) {
+            const prompt_len = generation_config.prompt_ids.length;
+            // @ts-expect-error TS2339
+            if (outputs.sequences) {
+                // @ts-expect-error TS2339
+                outputs.sequences = outputs.sequences.slice(null, [prompt_len, null]);
+            } else {
+                // @ts-expect-error TS2339
+                outputs = outputs.slice(null, [prompt_len, null]);
+            }
+        }
+
         if (generation_config.return_token_timestamps) {
             outputs['token_timestamps'] = this._extract_token_timestamps(
                 // @ts-expect-error TS2345