# Reported issues for obsidian-mcp-server

Pod holds 21 of 32 problems reported by people outside the maintainer team. Issues filed by the project's own owners, members and collaborators are excluded entirely — a maintainer's release checklist is not a warning to a prospective user.

Back to [obsidian-mcp-server](/mcp/obsidian-mcp-server).

## Most discussed

### bug: tool schemas declare JSON Schema draft-07 dialect — strict clients reject every tool call before it reaches the server

### Server version

3.2.12 (via npx -y obsidian-mcp-server, 2026-08-15)

### mcp-ts-core version

^0.11.1 (per obsidian-mcp-server@3.2.12 package.json)

### Runtime

Node.js

### Runtime version

Node (Homebrew, macOS arm64), launched via npx — exact version not captured

### Transport

stdio

### OS

macOS (Apple Silicon)

### Description

Every tool this server exposes declares its `inputSchema`/`outputSchema` with `"$schema": "http://json-schema.org/draft-07/schema#"`. Clients that strictly e

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/109) · 2026-08-15 · closed · external user · 4 comments

### All tools return "Structured content does not match tool output schema" in 3.2.x (worked in 3.1.4)

### Server version

3.2.8

### mcp-ts-core version

0.10.9

### Runtime

Node.js

### Runtime version

24.18.0

### Transport

stdio

### OS

Windows 11

### Description

## Description
After upgrading from 3.1.4 → 3.2.x, all tools fail with structured content schema 
validation errors. The server appears to be running and connected, but every tool 
call is rejected by the MCP client before returning any result.

Downgrading to 3.1.4 resolves the issue immediately.

## Environment
- obsidian-mcp

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/87) · 2026-06-24 · closed · external user · 3 comments

### path_forbidden response shape violates tool output schema, surfaces as opaque MCP error

### Server version

3.2.0

### mcp-ts-core version

0.9.1

### Runtime

Node.js

### Runtime version

Node 22.x

### Transport

stdio

### OS

macOS 15.x

### Description

When a write is denied by the folder-scoped permissions (`OBSIDIAN_WRITE_PATHS` / `OBSIDIAN_READ_PATHS` / `OBSIDIAN_READ_ONLY`), the response body returned by the server is missing fields that the tool's own output schema declares as required. The MCP runtime then rejects the response as schema-invalid, and clients see a gener

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/66) · 2026-05-21 · open · external user · 5 comments

### feat(auth): allow opt-out of per-tool scope enforcement for OIDC providers that can't inject custom scopes

### Use case

**Who benefits:** operators self-hosting `obsidian-mcp-server` with HTTP transport behind a standard OIDC authorization server (Authentik, Keycloak < 26.5, Zitadel, etc.) and consuming it from MCP clients that don't allow scope customization (Claude.ai, ChatGPT, etc.).

**Problem:** the framework's `withRequiredScopes` check (`@cyanheads/mcp-ts-core` → `dist/mcp-server/transports/auth/lib/authUtils.js`) enforces per-tool scopes formatted as `tool:<NAME>:<read|write>` on every tool 

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/47) · 2026-05-09 · closed · external user · 3 comments

### Obsidian MCP Server Initialization Timeout with Claude for Desktop

Obsidian MCP Server Initialization Timeout with Claude for Desktop

### Description
The Obsidian MCP server starts successfully but consistently times out after exactly 60 seconds during the initialization phase. The initialization request never completes successfully, preventing the server from registering any tools for use with Claude for desktop.

### Environment
Windows 11
Node.js v22.11.0
obsidian-mcp-server version 1.5.8
Obsidian Local REST API plugin version 3.1.0
Obsidian version 1.8.10

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/9) · 2025-05-05 · closed · external user · 3 comments

### Glama listing is missing Dockerfile

Your MCP server is currently listed on the [Glama MCP directory](https://glama.ai/mcp/servers/cyanheads/obsidian-mcp-server), but it is not available for others to use because it does not have a Dockerfile.

It takes only a few minutes to fix this:

1. Go to your server's listing: [cyanheads/obsidian-mcp-server](https://glama.ai/mcp/servers/cyanheads/obsidian-mcp-server)
2. Click "Claim" to verify ownership.
3. Once claimed, navigate to the [admin `Dockerfile` page](https://glama.ai/mcp/servers/

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/6) · 2025-04-20 · closed · external user · 3 comments

### Stuck at waiting for server to respond to initialize request

Hello,

I have some problems to get the MCP Server to work. I have set up my Obsidian with the Local REST API, configured it as HTTP for now for testing.

My config of the server is this:
```
..
  "VERIFY_SSL": "false",
  "OBSIDIAN_PROTOCOL": "http",
  "OBSIDIAN_HOST": "127.0.0.1",
  "OBSIDIAN_PORT": "27123",
  "REQUEST_TIMEOUT": "5000",
  "MAX_CONTENT_LENGTH": "52428800",
  "MAX_BODY_LENGTH": "52428800",
  "RATE_LIMIT_WINDOW_MS": "900000",
  "RATE_LIMIT_MAX_REQUESTS": "200",
  "TOOL_TIMEOUT_MS"

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/5) · 2025-04-10 · closed · external user · 8 comments

### Error msg from Claude desktop:  Expected ',' or ']' after array element in JSON at position 5 (line 1 column 6)

## Issue Description
When starting the Claude desktop app, the MCP server encounters a specific JSON parsing error:

**Error Message:** `Expected ',' or ']' after array element in JSON at position 5 (line 1 column 6)`

This error occurs during communication between the Claude desktop app and the obsidian-mcp-server when attempting to list resources.

## Error Logs
```
2025-03-16T06:12:50.065Z [obsidian-mcp-server] [info] Message from client: {"method":"prompts/list","params":{},"jsonrpc":"2.0","

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/4) · 2025-03-16 · closed · external user · 3 comments

## Most recent

### serializeFrontmatter: CRLF rewrites create mixed EOLs and empty-block removal strips body indentation

Two correctness problems in `serializeFrontmatter` on 3.5.0.

**3a — CRLF frontmatter rewrites create mixed-EOL files.** An effective frontmatter mutation that leaves a non-empty mapping reserializes the YAML with LF: `doc.toString()` emits LF and `serializeFrontmatter` also hard-codes LF around the fences. A CRLF note therefore ends up with an LF frontmatter block while its verbatim body stays CRLF. The block's original EOL should be applied to both the serialized YAML and the fence delimiters.

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/125) · 2026-08-26 · open · external user · 0 comments

### YAML aliases and scalar-root frontmatter cause generic -32603 failures in obsidian_manage_frontmatter / obsidian_manage_tags

In v3.5.0 the mutation helpers do not consistently handle frontmatter that cannot be mutated safely: some cases escape as exceptions instead of producing a controlled result. `frontmatterParseError()` reports the first `doc.errors` entry and non-null, non-mapping YAML roots, but neither `deleteFrontmatterKey()` nor `mutateFrontmatterTags()` calls it. In the two delete reproductions below, unresolved aliases pass `parseDocument()` with an empty `doc.errors`; deleting an anchor owner can create th

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/124) · 2026-08-26 · open · external user · 0 comments

### Silent data loss: frontmatter helpers destroy content on invalid YAML and drop non-string entries from tags arrays

Two write paths in `frontmatter-ops.ts` can silently destroy user content on 3.5.0.

**1a — `deleteFrontmatterKey` can wipe the entire block when the YAML is invalid.**
```md
---
a: "unterminated
keep: yes
---
Body
```
Call `obsidian_manage_frontmatter` with `operation: "delete"` and `key: "a"`. Observed: the helper returns exactly `Body\n`; `keep: yes` and the entire frontmatter block are gone, and the tool writes that changed content back. `parseDocument` records an entry in `doc.errors` and r

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/123) · 2026-08-26 · open · external user · 0 comments

### 404 errors from #request print the un-doubled path, hiding the real requested URL

Companion to #121. Filing separately because it is an independent correctness bug in the error path — it would be worth fixing even if #121 were resolved, and it is what made #121 expensive to diagnose.

Verified against v3.5.0 as installed via `npx`.

### Cause

`dist/services/obsidian/obsidian-service.js:591`, inside `#request`'s `exec` closure:

```js
if (!res.ok) {
    await this.#throwForStatus(res, pathAndQuery, ctx);
}
```

This passes `pathAndQuery` — the path *before* concatenation with

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/122) · 2026-08-24 · open · external user · 0 comments

### Trailing slash in OBSIDIAN_BASE_URL 404s every endpoint (unnormalized concatenation)

If `OBSIDIAN_BASE_URL` is set with a trailing slash, **every** endpoint 404s, because the base URL and path are concatenated without normalization.

Verified against v3.5.0 (`package.json` confirms the version) as installed via `npx`.

### Cause

`dist/services/obsidian/obsidian-service.js:577`, inside the private `#request` method:

```js
#request(ctx, pathAndQuery, init) {
    const url = `${this.#config.baseUrl}${pathAndQuery}`;
```

Plain template-string concatenation — no `new URL(path, bas

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/121) · 2026-08-24 · open · external user · 0 comments

### bug: every tool's structuredContent fails strict outputSchema validation (-32602) — 3.2.8 through 3.2.12

### Summary

On every version tested between 3.2.8 and 3.2.12 (current), tools return `structuredContent` that does not conform to their declared `outputSchema`. A strict MCP client — one that validates `structuredContent` against the tool's `outputSchema` per the 2025-06-18 spec — rejects every call with JSON-RPC `-32602`. As of 3.2.12 this affects **all** read tools I can exercise (`get_note`, `list_notes`, `search_notes` in both `text` and `jsonlogic` modes), making the server unusable from a

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/108) · 2026-08-08 · closed · external user · 2 comments

### obsidian_patch_note/obsidian_append_to_note reject valid heading-section calls with a structured-content schema error, and the edit silently doesn't apply

Both `obsidian_patch_note` (operation: append, section type: heading) and `obsidian_append_to_note` (section type: heading) fail against an existing note with an existing heading, on two separate notes:

`obsidian_patch_note` error:
```
Structured content does not match the tool's output schema: data must have required property 'path', data must have required property 'section', data must have required property 'operation', data must have required property 'previousSizeInBytes', data must have r

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/101) · 2026-08-02 · closed · external user · 1 comment

### bug(stdio-transport): server process leaks as orphan (ppid=1) when MCP client disconnects

## Summary

`obsidian-mcp-server` child processes (started over stdio transport by MCP clients such as Claude Code CLI) do not exit when the parent/client session ends. They only disappear if stdin is closed or the parent dies outright — otherwise they are silently re-parented (`ppid=1`, adopted by `launchd`/`init`) and keep running indefinitely. There does not appear to be any self-liveness check (e.g. polling for parent death, or exiting on stdin EOF) in the stdio transport path.

## Evidence

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/100) · 2026-08-02 · closed · external user · 1 comment

### obsidian_open_in_ui can create files under OBSIDIAN_READ_ONLY=true

Thanks for this server — the path scoping and the `read_only` kill switch are exactly what we needed
for a read-only vault integration.

We hit a case where a file was created in the vault while `OBSIDIAN_READ_ONLY=true` was active.

## Environment

- `obsidian-mcp-server` **3.2.9** (via `npx`)
- Obsidian **1.13.4**, Local REST API plugin (HTTPS on `127.0.0.1:27124`)
- Client: Claude Desktop (macOS 15)
- Config: `OBSIDIAN_READ_ONLY=true`, `OBSIDIAN_ENABLE_COMMANDS=false`, no `OBSIDIAN_WRITE_PATH

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/99) · 2026-08-01 · closed · external user · 2 comments

### obsidian_write_note fails when Obsidian-mcp-server is connected through MCPO to Open WebUI

### Server version

3.2.9

### mcp-ts-core version

0.10.10

### Runtime

Bun

### Runtime version

1.3.14

### Transport

HTTP (Streamable HTTP)

### OS

Windows / Docker Desktop

### Description

obsidian_write_note fails with "Invalid input: expected object, received string" when Obsidian-mcp-server is connected through MCPO to Open WebUI.

### Steps to reproduce

Call the tool from within the chat in Open WebUI to create a test note.

### Actual behavior

```shell
The error returned from the

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/91) · 2026-07-16 · open · external user · 2 comments

### jsonlogic returning output that does not conform to the schema

### Server version

3.2.8

### mcp-ts-core version

0.10.9

### Runtime

Node.js

### Runtime version

24.16.0

### Transport

stdio

### OS

macOS Tahoe 26.5

### Description

## Title

`get_note`, `list_notes`, and `jsonlogic` search return structuredContent that fails strict outputSchema validation (3.2.8)

---

## Body

### Summary

On v3.2.8, several tools return `structuredContent` that does not conform to their declared `outputSchema`. A strict MCP client (one that validates `structuredC

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/90) · 2026-06-30 · closed · external user · 1 comment

### feat(service): deny-list functionality

### Use case

Hello. Thank you for this project. I have a configuration feature request:

The current configuration is focused on "I want the AI to access only those few folders/notes in my large vault". However, my use case is the other way around: "I want the AI to access everything BUT those few folders." 

### Proposed behavior

Add `OBSIDIAN_DENY_PATHS`. It works similar to `OBSIDIAN_READ_PATHS` and `OBSIDIAN_WRITE_PATHS` but in the other direction and can be used together (allow a folder, 

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/76) · 2026-06-02 · open · external user · 2 comments

### obsidian_search_notes: dataview mode advertised in README but absent from v3.2.0 tool schema

### Server version

3.2.0

### mcp-ts-core version

0.9.1

### Runtime

Node.js

### Runtime version

Node 22.x

### Transport

stdio

### OS

macOS 15.x

### Description

The README's `obsidian_search_notes` section advertises three search modes: `text`, `dataview`, and `jsonlogic`. The v3.2.0 tool schema's `mode` enum only exposes two: `["text", "jsonlogic"]`. Attempts to call with `mode: "dataview"` fail at the MCP input-validation stage before reaching the server.

### Steps to reproduce

1.

[Read the thread](https://github.com/cyanheads/obsidian-mcp-server/issues/67) · 2026-05-21 · closed · external user · 2 comments

The remaining reports are on [the project's issue tracker](https://github.com/cyanheads/obsidian-mcp-server/issues).