Best tools for organizing PDFs in Obsidian

A 127GB pile of RPG rulebooks and reference PDFs was slipping through a highlight-and-notes workflow built around ebooks, because PDFs mix “fiction” text with “reference” material that doesn’t fit neatly into typical annotation flows. The solution that finally matched the creator’s needs is Zotero—used as the PDF library and metadata engine—then wired into Obsidian so PDFs become searchable, taggable, and clickable down to specific pages.

The requirements were practical rather than academic. Citations mattered little; the priority was organizing by tags and categories (so RPG elements like character options, adventures, and bestiaries could be queried later in Obsidian via Dataview), plus “processing” that still allows reading and annotating on mobile or other devices. Just as important were two reference features: deep links that open a PDF at the right page from inside Obsidian, and the ability to keep copies locally and in the cloud (notably Dropbox) while syncing across macOS, Linux, iPad, and Android. Sharing with other gamers also mattered.

Trying to do everything inside Obsidian ran into hard limits. Obsidian handles references well when PDFs are stored as vault assets—hash-based links can open a PDF at a specific page, enabling a table-of-contents style experience. But PDFs aren’t easily categorized because they aren’t markdown notes, and PDF reading/annotation support is not robust enough without extra plugins.

Several alternatives failed on key constraints. DEVONthink could tag and deep-link, but annotation couldn’t be carried into Obsidian, and syncing with Dropbox/iCloud triggered repeated indexing and file-state errors. It also pushed the workflow toward “local-only,” and its mobile companion (DEVONthink To Go) is iOS-only, making cross-device use with Android unrealistic. Readwise performed strongly for highlighting and exporting highlights into Obsidian, but it wasn’t designed as a PDF repository: tagging within the PDF library was effectively read-only, deep links weren’t reliable, and sharing PDFs wasn’t a core strength.

A macOS-focused approach—Skim plus file tagging—worked for lightweight deep links and quick annotation, but it tied the system to macOS and didn’t handle cloud-only PDFs well. That meant online-only files wouldn’t be consistently available, and sharing/tag portability across different operating systems remained weak.

Zotero, by contrast, hit the full checklist, with one tradeoff: the integration relies on Zotero plugins rather than Obsidian plugins. The workflow uses Zotero libraries/collections to categorize RPG PDFs, then uses plugins to import folders automatically and to copy Zotero tags into Obsidian. For page-level reference, Zotero context-menu tools generate special “select item” links; with the right identifier syntax and page numbers, Obsidian links can open the exact PDF location. To avoid duplicating 127GB of files, Zotero is configured to use linked attachments pointing to a base directory (such as Dropbox). Finally, Obsidian becomes the database layer: tags and metadata flow in, Dataview queries surface structured lists (e.g., Arcadia magazine sections), and clicking a result jumps straight to the relevant page inside the PDF.

The end result turns “forgotten folders” into an actively usable RPG reference system—one that scales across devices and stays maintainable even outside an academic citation mindset.