Obsidian Sync Plugin

Jul 16, 20265 min read

The official Linkwise plugin syncs your saved links, AI summaries, highlights, and collections from Linkwise into your Obsidian vault as clean Markdown notes.

Sync is one-way (Linkwise → Obsidian), incremental (only what changed), and local-first - Linkwise keeps your summaries and highlights up to date, while anything you write in a note is never overwritten.

Connecting Obsidian with Linkwise

Open the Obsidian community plugin marketplace and search for "Linkwise".
Install and enable the plugin.
Connect - show the QR code in the Obsidian plugin settings and scan it with the Linkwise app (or paste the token manually).
Tap Sync now - done. Optionally turn on auto-sync.

Filtering what syncs

Linkwise syncs the links you've saved, organized by their collection. To control what lands in Obsidian, organize links into collections in the Linkwise app - each collection becomes a folder in your vault. (Fine-grained tag/status filters in the plugin are on the roadmap.)

Configuring sync

Set the auto-sync interval in the plugin settings:

Manual only (default) - syncs only when you run the command. Recommended if you like to control exactly when notes are written.
Every 15 / 30 / 60 / 180 minutes - the plugin pulls new changes on that schedule in the background.

Trigger a manual sync any time via:

The circular-arrows ribbon icon, or
Command palette (Cmd/Ctrl+P) → "Linkwise: Sync now", or
The Sync now button in settings.

Each item is tracked by a hidden linkwise_id, so re-syncing updates notes in place and never creates duplicates - even if you renamed or moved the note.

What your vault looks like

Linkwise/
  Research/
    Research.md                 ← index note ("Map of Content"), named after the collection
    Agent Harness Engineering.md
    Attention Is All You Need.md
  Unsorted/                     ← links you haven't filed into a collection yet
    Unsorted.md
    …

The index note is named after its collection (e.g. Research.md), so in the graph view its hub node reads as the collection name rather than a generic label.

Each note:

---
linkwise_id: "cf2cf531-…"      ← don't edit; this is how sync tracks the note
title: "Agent Harness Engineering"
url: "https://addyosmani.com/blog/agent-harness-engineering/"
source: "addyosmani.com"
collection: "Research"
tags: [ai, agents]
highlight_colors: [yellow, purple]   ← the highlight colors used in this note
saved: 2026-06-16
cover: "https://…"
---

## Summary

…the AI-generated summary…

## Key questions

**A question the article answers**

…the AI-generated answer…

## Highlights


a passage you highlighted in Linkwise


*your annotation on that highlight*

## My notes
Write anything you want here — it's yours and survives every re-sync.

Each highlight renders as a colored block whose left bar matches the color you used in Linkwise (yellow, purple, pink, blue, or green), with a faint tint behind it. Any annotation you wrote appears in italics just beneath.

Filter by highlight color

The highlight_colors property lists the colors present in a note, so you can find notes by color:

Search: ["highlight_colors":yellow] in the search bar.
Dataview: FROM "Linkwise" WHERE contains(highlight_colors, "yellow")
Bases / Properties view: filter or group on the highlight_colors property.

The golden rule: ## My notes is your space

Everything above ## My notes is managed by Linkwise (frontmatter, the source callout, summary, and highlights). Linkwise keeps this up to date on every sync.

Everything from ## My notes down is yours. Write your own thoughts, add sections, link to other notes - it's preserved forever. Just keep the ## My notes heading in place as the divider.

You can freely rename or move notes; they're matched by linkwise_id, not the filename.

Note: don't edit or remove the linkwise_id field - it's how the plugin tracks each note. Deleting it can cause a duplicate to be created on the next sync.

Settings reference

Setting	What it does
Personal access token	The lw_pat_… token from the Linkwise app.
Vault folder	Root folder synced notes are written into (default Linkwise).
Auto-sync interval	How often to pull automatically; Manual only = on command.
When a link is deleted in Linkwise	Mark (default, keeps the note + adds linkwise_deleted: true), Trash (move to _trash), or Ignore. Never hard-deletes.
API base URL (advanced)	Only change if self-hosting/testing.
Reset sync state (advanced)	Forgets the cursor so the next sync re-pulls everything (merged by ID, no duplicates).

Managing the connection

Check status: the Integrations card in the app shows "Last synced …" and your token prefix.
Disconnect / revoke: Linkwise app → Integrations → Revoke. The plugin stops syncing immediately; notes already in your vault stay put.
Re-pull everything: Obsidian → Settings → Linkwise → Reset sync state → Sync now.

Troubleshooting

Symptom	Fix
"Invalid or revoked token"	Generate a fresh token in the app and paste it again.
"Obsidian sync is a Pro feature"	Your Linkwise Pro subscription isn't active.
Nothing synced / "already up to date"	No new changes since the last sync, or no saved links yet.
Notes didn't appear	Check the Vault folder setting and that the plugin is enabled.
I want to re-pull everything	Settings → Reset sync state → Sync now.
A highlight I deleted is still there	Known limit: a highlight removed on its own updates only when its article next changes.

Privacy & security

No telemetry or analytics - the plugin only talks to the Linkwise sync API.
Your token is stored in the plugin's data.json, inside your vault. If your vault is synced/shared, the token travels with it - it's read-only and revocable anytime from the app. Treat it like a password.
If the same vault syncs across devices, run Linkwise sync on one primary device to keep writes tidy.