diff --git a/paperqa/agents/__init__.py b/paperqa/agents/__init__.py
index d542c0162..9b45f0794 100644
--- a/paperqa/agents/__init__.py
+++ b/paperqa/agents/__init__.py
@@ -6,6 +6,7 @@
 from pathlib import Path
 from typing import Any
 
+from aviary.utils import MultipleChoiceQuestion
 from pydantic_settings import CliSettingsSource
 from rich.logging import RichHandler
 
@@ -97,7 +98,7 @@ def configure_cli_logging(verbosity: int | Settings = 0) -> None:
         print(f"PaperQA version: {__version__}")
 
 
-def ask(query: str, settings: Settings) -> AnswerResponse:
+def ask(query: str | MultipleChoiceQuestion, settings: Settings) -> AnswerResponse:
     """Query PaperQA via an agent."""
     configure_cli_logging(settings)
     return get_loop().run_until_complete(
@@ -109,7 +110,7 @@ def ask(query: str, settings: Settings) -> AnswerResponse:
 
 
 def search_query(
-    query: str,
+    query: str | MultipleChoiceQuestion,
     index_name: str,
     settings: Settings,
 ) -> list[tuple[AnswerResponse, str] | tuple[Any, str]]:
@@ -119,7 +120,7 @@ def search_query(
         index_name = settings.get_index_name()
     return get_loop().run_until_complete(
         index_search(
-            query,
+            query if isinstance(query, str) else query.question_prompt,
             index_name=index_name,
             index_directory=settings.agent.index.index_directory,
         )
diff --git a/paperqa/agents/main.py b/paperqa/agents/main.py
index 5f4532813..460bcfc3e 100644
--- a/paperqa/agents/main.py
+++ b/paperqa/agents/main.py
@@ -11,6 +11,7 @@
     ToolSelector,
     ToolSelectorLedger,
 )
+from aviary.utils import MultipleChoiceQuestion
 from pydantic import BaseModel
 from rich.console import Console
 from tenacity import (
@@ -49,12 +50,12 @@
 
 
 async def agent_query(
-    query: str | QueryRequest,
+    query: str | MultipleChoiceQuestion | QueryRequest,
     docs: Docs | None = None,
     agent_type: str | type = DEFAULT_AGENT_TYPE,
     **runner_kwargs,
 ) -> AnswerResponse:
-    if isinstance(query, str):
+    if isinstance(query, str | MultipleChoiceQuestion):
         query = QueryRequest(query=query)
     if docs is None:
         docs = Docs()