diff --git a/evals/debug_prompt.cc b/evals/debug_prompt.cc
index 8a4cc8f..7ea32fa 100644
--- a/evals/debug_prompt.cc
+++ b/evals/debug_prompt.cc
@@ -59,10 +59,13 @@ int Run(int argc, char** argv) {
   env.MutableConfig().layers_output =
       prompt_args.layers_output.Empty()
           ? LayersOutputFunc()
-          : [&json_output](int pos, const std::string& key, const float* values,
-                           size_t values_len) {
-              std::vector<float> v{values, values + values_len};
-              json_output[std::to_string(pos)][key] = v;
+          : [&json_output](size_t query_idx, size_t pos, const std::string& key,
+                           int layer, const float* values, size_t values_len) {
+              const std::string& debug_key =
+                  layer < 0 ? key : (key + "." + std::to_string(layer));
+              const std::vector<float> v{values, values + values_len};
+              json& json_base = json_output[std::to_string(query_idx)];
+              json_base[std::to_string(pos)][debug_key] = v;
             };
 
   const auto [answer, token_count] = env.QueryModel(prompt_args.prompt);
diff --git a/gemma/gemma-inl.h b/gemma/gemma-inl.h
index 0613b92..9992981 100644
--- a/gemma/gemma-inl.h
+++ b/gemma/gemma-inl.h
@@ -805,8 +805,10 @@ HWY_NOINLINE void Transformer(const int* tokens, size_t num_tokens,
   const size_t num_interleaved = num_tokens * num_queries;
   if (layers_output) {
     for (size_t token_idx = 0; token_idx < num_interleaved; ++token_idx) {
-      float token_f = tokens[token_idx];
-      layers_output(pos + token_idx, "Tokens", &token_f, 1);
+      const size_t query_idx = token_idx % num_queries;
+      const size_t logical_pos = (pos + token_idx) / num_queries;
+      const float token_f = tokens[token_idx];
+      layers_output(query_idx, logical_pos, "tokens", -1, &token_f, 1);
     }
   }
   constexpr size_t kModelDim = TConfig::kModelDim;
@@ -821,9 +823,9 @@ HWY_NOINLINE void Transformer(const int* tokens, size_t num_tokens,
                               layer_weights, activations, kv_caches, pool);
 
     if (layers_output) {
-      const std::string block_name = "blocks." + std::to_string(layer);
       for (size_t token_idx = 0; token_idx < num_interleaved; ++token_idx) {
-        layers_output(pos + token_idx, block_name,
+        const size_t logical_pos = (pos + token_idx) / num_queries;
+        layers_output(token_idx % num_queries, logical_pos, "blocks", layer,
                       activations.x.Batch(token_idx), kModelDim);
       }
     }
@@ -833,7 +835,9 @@ HWY_NOINLINE void Transformer(const int* tokens, size_t num_tokens,
                         activations.x.All(), kModelDim);
   if (layers_output) {
     for (size_t token_idx = 0; token_idx < num_interleaved; ++token_idx) {
-      layers_output(pos + token_idx, "final_norm",
+      const size_t query_idx = token_idx % num_queries;
+      const size_t logical_pos = (pos + token_idx) / num_queries;
+      layers_output(query_idx, logical_pos, "final_norm", -1,
                     activations.x.Batch(token_idx), kModelDim);
     }
   }
diff --git a/gemma/gemma.h b/gemma/gemma.h
index e734456..081e783 100644
--- a/gemma/gemma.h
+++ b/gemma/gemma.h
@@ -49,13 +49,15 @@ using AcceptFunc = std::function<bool(int, float)>;
 // If not empty, SampleFunc is called with the probability distribution for the
 // next token, and its return value is used as the next generated token.
 using SampleFunc = std::function<int(const float*, size_t)>;
-// Will be called for layers output with:
+// If not empty, LayersOutputFunc is called for layer outputs, specified with:
+// - index of query within containing batch (if any); zero otherwise.
 // - position in the tokens sequence
-// - name of the data, p.ex. "tokens", "block.1", "final_norm"
+// - name of the data, e.g. "tokens", "blocks", "final_norm"
+// - layer index (or -1 for global outputs), e.g. "blocks" exposes x per-layer
 // - pointer to the data array
 // - size of the data array
 using LayersOutputFunc =
-    std::function<void(int, const std::string&, const float*, size_t)>;
+    std::function<void(size_t, size_t, const std::string&, int, const float*, size_t)>;
 
 struct RuntimeConfig {
   bool StreamToken(size_t query_idx, size_t pos, int token, float prob) const {