# Zotero & Obsidian: Linking Your Reading Notes with MarkDB-Connect

If you use [Zotero](https://www.zotero.org/) to manage your references and a Markdown editor like [Obsidian](https://obsidian.md/) to take reading notes, you've probably run into the same friction: Zotero has no idea your notes exist. You can't see at a glance which papers you've already annotated, and jumping between a Zotero item and its corresponding note requires manual hunting.

MarkDB-Connect solves exactly this problem.

## What MarkDB-Connect Does

[MarkDB-Connect](https://github.com/daeh/zotero-markdb-connect) is a Zotero plugin that scans a folder of Markdown files and automatically adds a coloured tag to any Zotero item that has an associated reading note. It also lets you jump directly from a Zotero item to that note via the right-click context menu.

The result is a visual indicator — a coloured dot next to tagged items in your library — that tells you at a glance where you've done the intellectual work.

The plugin was built primarily with Obsidian in mind, but also supports [Logseq](https://logseq.com/) and [Zettlr](https://www.zettlr.com/), and can work with any Markdown-based workflow that stores notes outside Zotero.

## How It Works Under the Hood

The plugin needs a way to match a Markdown file to a specific Zotero item. There are two approaches:

**Option 1: Better BibTeX citekeys.** This is the recommended route if you're already using [Better BibTeX](https://retorque.re/zotero-better-bibtex/) and tools like Obsidian Zotero Integration or BibNotes Formatter. The plugin can extract the citekey from the filename (e.g. `@smith2021cognition.md`), from the YAML frontmatter, or from the file body using a custom regex.

**Option 2: Zotero Item Keys.** If you created notes via Zotero's own Export Note feature, you can use the internal item key instead (e.g. `ABCD1234` from `zotero://select/library/items/ABCD1234`), again extracted with a custom regex pattern.

For most Obsidian users, Option 1 with filename-based citekeys is the path of least resistance.

## Installation

1. Download the `.xpi` file from the [latest release](https://github.com/daeh/zotero-markdb-connect/releases/latest)
2. In Zotero, go to **Tools → Plugins**
3. Click the gear icon and choose **Install Add-on From File...**
4. Select the downloaded `.xpi` file and restart Zotero

The plugin supports Zotero 7 and 8. (If you're still on Zotero 6, the last compatible release was v0.0.27.)

## Setting It Up: My Configuration

Once installed, open **Zotero Settings** and navigate to the **MarkDB-Connect** pane. The key things to configure:

- **The folder path** pointing to your Markdown reading notes (the plugin scans recursively, so subdirectories are fine)
- **How to extract the citekey** — by default it expects filenames starting with `@`, like `@smith2021.md`

*The MarkDB-Connect settings inside the Zotero Settings. My Obsidian Vault is configured.*

If you haven't set up the Zotero–Obsidian connection yet, [this guide walks you through the full workflow](https://citationstyler.com/en/knowledge/how-to-use-zotero-with-obsidian-knowledge-management/) and [this video by Paul Mayer](https://www.youtube.com/watch?v=8yMko1m8XSQ) shows it nicely also. MarkDB-Connect fits in as the final piece that closes the loop between your reference manager and your notes.

After that, run **Tools → MarkDB-Connect Sync Tags**. The plugin will scan your notes folder and add an `ObsCite` tag to every matched Zotero item.

Then go to the **Tags** panel in Zotero, right-click `ObsCite` and assign it a colour. In my library I use blue — every item with a 🟦 tag has a reading note in Obsidian.


## Jumping from Zotero to Your Note

Once the tags are in place, **right-clicking** any tagged item gives you an option to open the associated Markdown file directly in Obsidian (or your default Markdown editor).


> :warning: **One small friction point:** recent Zotero builds show a security prompt every time you open an external link. You can suppress this by setting `security.external_protocol_requires_permission` to `false` in Zotero's Config Editor (Settings → Advanced → Config Editor).

## Who Is This For?

MarkDB-Connect is ideal if you maintain a proper reading note practice — meaning you write substantial notes on papers in an external editor, not just highlights inside Zotero. If your workflow is entirely within Zotero's built-in notes, the plugin adds little value. But if Obsidian or Logseq is your thinking environment, this plugin closes a real gap.

It's also worth noting that MarkDB-Connect is read-only with respect to Zotero: it only adds tags, it never modifies your references or metadata. That makes it low-risk to try.

## Conclusion

MarkDB-Connect is one of those plugins that does one thing and does it well. If you're already invested in a Zotero + Obsidian (or Logseq) workflow, the coloured tag system and the direct jump-to-note feature remove a small but persistent friction point. Setup takes maybe fifteen minutes, and the plugin is read-only with respect to your Zotero data — so there's very little risk in trying it.

If your note-taking lives entirely inside Zotero, this probably isn't for you. But if your thinking happens in Markdown, it's well worth it.

## Links & Further Reading

- [MarkDB-Connect on GitHub](https://github.com/daeh/zotero-markdb-connect) — source code, releases, and issue tracker
- [How to use Zotero with Obsidian](https://citationstyler.com/en/knowledge/how-to-use-zotero-with-obsidian-knowledge-management/) — a full walkthrough of the Zotero–Obsidian integration that MarkDB-Connect builds on
- [citationstyler.com/en/knowledge/](https://citationstyler.com/en/knowledge/) — My blog with more articles on Zotero, citation styles, and academic workflows