diff --git a/.semversioner/next-release/patch-20250319182609055856.json b/.semversioner/next-release/patch-20250319182609055856.json
new file mode 100644
index 0000000000..87cc8a25eb
--- /dev/null
+++ b/.semversioner/next-release/patch-20250319182609055856.json
@@ -0,0 +1,4 @@
+{
+  "type": "patch",
+  "description": "Added batching logic to the prompt tuning autoselection embeddings workflow"
+}
diff --git a/graphrag/api/prompt_tune.py b/graphrag/api/prompt_tune.py
index 0c09714825..92f6ba94f3 100644
--- a/graphrag/api/prompt_tune.py
+++ b/graphrag/api/prompt_tune.py
@@ -111,7 +111,7 @@ async def generate_indexing_prompts(
 
     # if max_retries is not set, inject a dynamically assigned value based on the number of expected LLM calls
     # to be made or fallback to a default value in the worst case
-    if default_llm_settings.max_retries == -1:
+    if default_llm_settings.max_retries < -1:
         default_llm_settings.max_retries = min(
             len(doc_list), language_model_defaults.max_retries
         )
diff --git a/graphrag/prompt_tune/loader/input.py b/graphrag/prompt_tune/loader/input.py
index 17af53ec98..fa49ebeeb9 100644
--- a/graphrag/prompt_tune/loader/input.py
+++ b/graphrag/prompt_tune/loader/input.py
@@ -6,12 +6,14 @@
 import numpy as np
 import pandas as pd
 
+from graphrag.cache.noop_pipeline_cache import NoopPipelineCache
 from graphrag.callbacks.noop_workflow_callbacks import NoopWorkflowCallbacks
 from graphrag.config.models.graph_rag_config import GraphRagConfig
 from graphrag.index.input.factory import create_input
+from graphrag.index.operations.embed_text.strategies.openai import (
+    run as run_embed_text,
+)
 from graphrag.index.workflows.create_base_text_units import create_base_text_units
-from graphrag.language_model.manager import ModelManager
-from graphrag.language_model.protocol.base import EmbeddingModel
 from graphrag.logger.base import ProgressLogger
 from graphrag.prompt_tune.defaults import (
     LIMIT,
@@ -21,20 +23,9 @@
 from graphrag.prompt_tune.types import DocSelectionType
 
 
-async def _embed_chunks(
-    text_chunks: pd.DataFrame,
-    embedding_llm: EmbeddingModel,
-    n_subset_max: int = N_SUBSET_MAX,
-) -> tuple[pd.DataFrame, np.ndarray]:
-    """Convert text chunks into dense text embeddings."""
-    sampled_text_chunks = text_chunks.sample(n=min(n_subset_max, len(text_chunks)))
-    embeddings = await embedding_llm.aembed_batch(sampled_text_chunks["text"].tolist())
-    return text_chunks, np.array(embeddings)
-
-
 def _sample_chunks_from_embeddings(
     text_chunks: pd.DataFrame,
-    embeddings,
+    embeddings: np.ndarray[float, np.dtype[np.float_]],
     k: int = K,
 ) -> pd.DataFrame:
     """Sample text chunks from embeddings."""
@@ -60,7 +51,6 @@ async def load_docs_in_chunks(
     embeddings_llm_settings = config.get_language_model_config(
         config.embed_text.model_id
     )
-
     dataset = await create_input(config.input, logger, root)
     chunk_config = config.chunks
     chunks_df = create_base_text_units(
@@ -88,18 +78,29 @@ async def load_docs_in_chunks(
         if k is None or k <= 0:
             msg = "k must be an integer > 0"
             raise ValueError(msg)
-        embedding_llm = ModelManager().register_embedding(
-            name="prompt_tuning_embeddings",
-            model_type=embeddings_llm_settings.type,
-            config=embeddings_llm_settings,
-            callbacks=NoopWorkflowCallbacks(),
-            cache=None,
-        )
 
-        chunks_df, embeddings = await _embed_chunks(
-            chunks_df, embedding_llm, n_subset_max=n_subset_max
+        """Convert text chunks into dense text embeddings."""
+        sampled_text_chunks = chunks_df.sample(n=min(n_subset_max, len(chunks_df)))[
+            "text"
+        ].tolist()
+
+        embedding_results = await run_embed_text(
+            sampled_text_chunks,
+            callbacks=NoopWorkflowCallbacks(),
+            cache=NoopPipelineCache(),
+            args={
+                "llm": embeddings_llm_settings.model_dump(),
+                "num_threads": embeddings_llm_settings.concurrent_requests,
+                "batch_size": config.embed_text.batch_size,
+                "batch_max_tokens": config.embed_text.batch_max_tokens,
+            },
         )
+        embeddings = np.array(embedding_results.embeddings)
         chunks_df = _sample_chunks_from_embeddings(chunks_df, embeddings, k=k)
 
     # Convert the dataset to list form, so we have a list of documents
-    return chunks_df["text"].tolist()
+    return [
+        # need this to prevent the str.format() function from breaking when parsing LaTeX from markdown files
+        i.replace("{", "{{").replace("}", "}}")
+        for i in chunks_df["text"]
+    ]