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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.

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 · 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 · 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 · 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 · 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 · 2025-05-05 · closed · external user · 3 comments

Glama listing is missing Dockerfile

Your MCP server is currently listed on the Glama MCP directory, 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
  2. Click "Claim" to verify ownership.
  3. Once claimed, navigate to the [admin Dockerfile page](https://glama.ai/mcp/servers/

Read the thread · 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 · 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 · 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 · 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.

---
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 · 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:

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

This passes pathAndQuery — the path before concatenation with

Read the thread · 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:

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

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

Read the thread · 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 · 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).