Why Zotero needs an export step
Modern Zotero can store PDF annotations in its own database. The original attachment may therefore lack highlights that appear in the Zotero reader.
Before using another tool to extract highlights, create a PDF copy with those annotations embedded. That copy is the file you import.
Export the annotated PDF
From the Zotero library view, select the PDF attachment or item and use File > Export PDF. The PDF reader's Save As command can also create a copy with annotations included.
Save the exported PDF somewhere easy to find, such as a project folder for the paper, case, or literature review you are working on.
- Select the Zotero item or PDF attachment.
- Use Export PDF or Save As to create an annotated copy.
- Open the exported copy outside Zotero to confirm the highlights are visible.
- Import the exported copy into PDF Highlights App.
Keep citation context nearby
Keep bibliographic metadata and citations in Zotero. The exported PDF is the annotated source file for extraction, while the Zotero item remains the citation record.
When you export highlights later as Markdown, CSV, or JSON, keep the PDF name and page number fields enabled so you can reconnect each quote to the Zotero record while writing.
Common Zotero gotchas
Dragging the original attachment out of Zotero can produce a clean PDF without Zotero's database-backed annotations. Use the annotated export path.
Highlights visible in Zotero but absent from the exported PDF point to the wrong export path. Re-open the PDF in Zotero, use the reader's Save As or export command, then test the copy in Preview or Acrobat.