diff --git a/packages/zotero-mcp/package.nix b/packages/zotero-mcp/package.nix
index b62be92..d7042d5 100644
--- a/packages/zotero-mcp/package.nix
+++ b/packages/zotero-mcp/package.nix
@@ -88,9 +88,16 @@ python3Packages.buildPythonApplication rec {
     httpx
     unidecode
     bibtexparser
+    # Runtime deps for the annotation/layout/read tools (upstream "pdf" extra).
+    # nix's optional-dependencies is passthru-only and installs nothing, so
+    # anything needed at runtime must live in this list.
+    pymupdf
+    ebooklib
   ];
 
-  # Optional extras (semantic search, PDF, scite)
+  # Optional extras (semantic search, PDF, scite).
+  # NOTE: buildPythonApplication stores these in passthru only and does NOT
+  # install them; adding an extra here has no runtime effect.
   optional-dependencies = with python3Packages; {
     semantic = [
       chromadb