Find the annotated PDF export command
Mendeley has used several desktop interfaces, so menu labels vary. Look for an export command that names annotations, such as Export PDF with Annotations or Export with Annotations.
In Mendeley Reference Manager, check the file details for the PDF and look for the file options menu. In older Mendeley Desktop workflows, the export-with-annotations command may appear from the File menu or a right-click menu.
Export before extracting
Save the annotated PDF outside Mendeley's library sync location. Use a project folder so the exported file is distinct from the stored attachment.
Open the exported file in another PDF reader. Visible highlights and comments show that it is ready for import.
- Open the PDF in Mendeley.
- Use the export-with-annotations option available in your Mendeley version.
- Save the annotated copy to a project folder.
- Confirm the exported PDF shows the highlights outside Mendeley.
- Import that exported PDF into PDF Highlights App.
Batch export carefully
Export a large library in small batches and check a few files from each batch. Mendeley libraries often mix downloaded PDFs, linked files, missing files, and records without full text.
Keep verified annotated PDFs in one folder. It is far easier to audit than a library dump with uncertain annotation coverage.
Missing annotations in an export
A PDF that opens without highlights came from the wrong export path. Return to Mendeley and use the annotation-specific export command; copying the stored PDF can produce a clean file.
Some Mendeley versions do not expose an annotated export for every file. Open the PDF in a reader that displays the annotations, save a new annotated copy there, and import that copy.