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Migration Guide: Switch to MoLOS

Moving to a new productivity tool can feel overwhelming. We've designed this guide to make your transition from Notion, Obsidian, Logseq, or other tools as smooth as possible.

What to Expect​

MoLOS offers a unique approach: local-first data with native AI integration via MCP (Model Context Protocol). This means:

  • ✅ Your data stays on your device—no cloud dependencies
  • ✅ AI agents can read and write your tasks, notes, and documents automatically
  • ✅ Works offline, syncs on your terms
  • ✅ Full control over your data with SQLite database backups

Migration Time Estimates:

  • Light user (minimal data): 15–30 minutes
  • Moderate user (regular productivity use): 30 minutes–2 hours
  • Power user (complex workflows, years of data): 2–4 hours

You don't have to migrate everything at once. Start with what's critical, and move the rest gradually.

Preparation​

Before You Begin​

  1. Backup Everything

    • Export your data from your current tool
    • Keep the backup safe during migration
    • Don't delete anything until you're confident in MoLOS

  2. Install MoLOS

    • Follow the Quick Start Guide to get MoLOS running
    • Make sure MoLOS is accessible at http://localhost:4173 (or your configured port)
    • Test the basic modules: Tasks, Markdown, Quick Notes

  3. Document Your Workflow

    • Take screenshots of your current setup
    • Note the features you use most
    • Identify what's critical to migrate first

  4. Clear Time for Migration

    • Block off uninterrupted time (30 minutes to 2 hours for most users)
    • Have both tools running side-by-side during migration
    • Keep a notepad handy for questions or observations

From Notion​

Notion users often have complex workspaces with databases, pages, and rich content. Here's how to make the move.

Exporting from Notion​

  1. Open your Notion workspace
  2. Click the "..." menu (three dots next to your workspace name)
  3. Select "Export all as..."
  4. Choose export format:
    • Markdown & CSV — Recommended for best MoLOS compatibility
    • HTML — Use if you need formatting preserved (requires manual cleanup)
  5. Wait for the download to complete (can take several minutes for large workspaces)
  6. Extract the downloaded ZIP file

What You'll Get:

  • Markdown files for all pages and content
  • CSV files for databases (tasks, projects, etc.)
  • Attachments folder (images, files)

Importing to MoLOS​

Step 1: Import Documents (Pages)

  1. Navigate to the MoLOS-Markdown module
  2. Create a folder structure that matches your Notion workspace:
    • Documents/ for general pages
    • Projects/ for project-related content
  3. Upload your Markdown files:
    • Drag and drop files into the MoLOS-Markdown interface
    • Or click "Create Page" and paste Markdown content directly

Step 2: Import Databases (Tasks)

Notion databases require a bit more work. Here's your approach:

Option A: Manual Recreation (Recommended for Most Users)

  1. Open your Notion CSV export in a spreadsheet or text editor
  2. Identify key fields: title, status, tags, due dates, assignees
  3. Map to MoLOS structure:
    • Create Areas in MoLOS-Tasks for your Notion workspaces
    • Create Projects within those Areas
    • Create Tasks with appropriate statuses and priorities

Example Mapping:

Notion ConceptMoLOS Equivalent
WorkspaceArea
PageMarkdown Page
DatabaseProject with Tasks
Status propertyTask status (todo, in_progress, done)
Priority propertyTask priority (urgent, high, medium, low)
Due date propertyTask dueDate
TagsTask labels
AttachmentsMove to local storage, link from Markdown

Option B: Automated Migration Script (Technical Users)

MoLOS provides a Python script to help automate Notion CSV migration:

# Install dependencies
pip install requests pandas

# Run migration script
python scripts/migrate-from-notion.py \
  --notion-csv path/to/notion-export.csv \
  --molos-api-url http://localhost:4173 \
  --molos-api-key YOUR_API_KEY_HERE

# What the script does:
# 1. Reads Notion CSV export
# 2. Maps Notion properties to MoLOS Task fields
# 3. Creates Areas, Projects, and Tasks via MoLOS MCP API
# 4. Links relevant Markdown pages to Tasks

Note: The migration script is optional. Manual recreation gives you more control and helps you learn MoLOS structure.

Common Notion Migration Challenges​

Challenge: "Notion databases have complex relationships and lookups"

Solution: MoLOS uses a simpler hierarchy (Areas → Projects → Tasks). Simplify your structure:

  • Document relationships in Markdown notes
  • Use MoLOS task dependencies for critical relationships
  • Accept that some complex lookups may not translate perfectly

Challenge: "Rich text formatting is lost in Markdown export"

Solution: This is expected. MoLOS uses standard Markdown:

  • Bold, italics, lists, and tables will be preserved
  • Custom colors, highlights, and Notion-specific embeds won't translate
  • Focus on content over formatting—Markdown is more portable long-term

Challenge: "I have hundreds of attachments to import"

Solution:

  • Move attachments to your local file system
  • Link from Markdown pages: ![alt text](/path/to/file.jpg)
  • Consider hosting large files externally if storage is limited

From Obsidian​

Obsidian users typically have vaults of Markdown notes with linking systems. Migration is generally straightforward.

If you use Obsidian with cloud sync:

  1. Install the "Obsidian to MoLOS" plugin from the Obsidian community marketplace
  2. Configure the plugin with your MoLOS server URL:
    • Server: http://localhost:4173
    • API Key: Get from MoLOS settings (if authentication is enabled)
  3. Click "Sync to MoLOS" in the Obsidian plugin panel
  4. Select content to sync:
    • Entire vault
    • Specific folders
    • Tagged notes only
  5. Wait for sync to complete

Benefits of Plugin Approach:

  • Automatic bidirectional sync (changes in Obsidian reflect in MoLOS)
  • Preserves Obsidian's [[WikiLinks]] syntax
  • Ongoing sync (not just one-time migration)

Manual Export & Import​

If you prefer manual migration or the plugin isn't available:

Step 1: Export from Obsidian

  1. Open your Obsidian vault in your file explorer
  2. Copy the entire vault folder (or specific folders you want to migrate)
  3. Keep folder structure intact

Step 2: Import to MoLOS

  1. Stop your MoLOS Docker container (if using Docker): 
    docker-compose down
  2. Copy your Obsidian vault to MoLOS data directory: 
    cp -r /path/to/obsidian-vault ~/.molos/data/obsidian-vault/
  3. Start MoLOS: 
    docker-compose up -d
  4. Navigate to the MoLOS-Markdown module
  5. Your Obsidian vault should appear in the file tree

Obsidian to MoLOS Mapping​

Obsidian ConceptMoLOS Equivalent
VaultMarkdown Documents (entire vault or folders)
FolderMarkdown Folder/Path
NoteMarkdown Page
[[WikiLinks]]Markdown links (auto-converted by plugin, or manually)
TagsMarkdown Tags (preserve #tag syntax)
FrontmatterPage metadata or first heading
Embeds ![[note]]Markdown links or manual re-creation

Common Obsidian Migration Challenges​

Challenge: "Obsidian's [[WikiLinks]] syntax doesn't work in MoLOS"

Solution:

  • Use the MoLOS plugin for auto-conversion
  • Or manually replace [[Note Name]] with [Note Name](./note-name.md)
  • MoLOS-Markdown supports standard Markdown links

Challenge: "Frontmatter properties are important to my workflow"

Solution:

  • MoLOS-Markdown pages support YAML frontmatter for metadata
  • Alternatively, use first heading as title and document properties in description
  • For task properties, consider using MoLOS-Tasks instead of frontmatter

Challenge: "I use Obsidian plugins extensively"

Solution:

  • Manually recreate plugin functionality with MoLOS modules
  • Use MoLOS-Tasks for task management plugins
  • Use MoLOS-Markdown for note-taking plugins
  • Consider building a custom MoLOS module for specialized needs

From Logseq​

Logseq users have graph-based structures with journals and pages. Migration requires some restructuring.

Exporting from Logseq​

  1. Open Logseq
  2. Click the "..." menu (top-right corner)
  3. Select "Export all..."
  4. Choose export format:
    • OPML — Recommended for best compatibility
    • Markdown — Alternative, may require more cleanup
  5. Wait for the download to complete
  6. Extract the downloaded files

Importing to MoLOS​

Step 1: Create Folder Structure

  1. Navigate to MoLOS-Markdown module
  2. Create a structure that mimics your Logseq graph:
    • Journal/ for daily notes
    • Pages/ for static pages
    • Projects/ for project-related pages
  3. Upload Markdown/OPML files:
    • Drag and drop entire folder
    • Or import file-by-file for more control

Step 2: Convert Logseq Blocks to Markdown

Logseq's block-based structure is unique. Here's how to adapt:

<!-- Logseq block structure (converted) -->
## Daily Note - 2026-03-21

- Task 1: Review PR #123
  - Subtask 1: Check tests
  - Subtask 2: Verify docs

- Task 2: Write migration guide
  - [[Reference: Obsidian Plugin Docs]]
<!-- Equivalent MoLOS structure -->
## Daily Note - 2026-03-21

**Tasks:**
- Review PR #123
  - Check tests
  - Verify docs

- Write migration guide
  - [Reference: Obsidian Plugin Docs](./obsidian-plugin-docs.md)

Tip: For tasks, consider moving them to MoLOS-Tasks for better tracking.

Logseq to MoLOS Mapping​

Logseq ConceptMoLOS Equivalent
GraphMarkdown Tree (folders + pages)
Journal entryMarkdown Page with date in path or title
PageMarkdown Page
BlockMarkdown content (list items, paragraphs)
Block ref ((uuid))Markdown link or manual reference
Property property:: valueTask field or metadata in frontmatter
Query viewsMoLOS saved views/filters (for tasks)

Common Logseq Migration Challenges​

Challenge: "Logseq's block-based structure is lost in Markdown"

Solution:

  • Accept that MoLOS uses linear Markdown, not blocks
  • Use blockquotes > for content that needs visual separation
  • For tasks, migrate to MoLOS-Tasks for better organization
  • Consider that linear structure may be simpler and more maintainable

Challenge: "Query-based views (Journals, etc.) don't exist in MoLOS"

Solution:

  • Re-create views using MoLOS-Tasks filters and saved views
  • For journal-like browsing, use MoLOS-Markdown's hierarchical tree
  • Use tags and categories for organization

Challenge: "Block references and linking are different"

Solution:

  • Use Markdown links instead of block references
  • Document relationships in page descriptions
  • Use MoLOS-Tasks dependencies for task relationships

Migration Best Practices​

Before You Migrate​

✅ Backup Everything

  • Export complete data from source tool
  • Keep backup safe during migration
  • Don't delete source data until confident

✅ Document Your Workflow

  • Screenshot your current setup for reference
  • Note features you use daily
  • Identify what's critical to migrate

✅ Clean Up

  • Archive or delete unnecessary content before migrating
  • Consolidate similar items
  • Make migration easier by reducing clutter

✅ Test MoLOS

  • Have MoLOS running and accessible
  • Test basic modules (Tasks, Markdown, Quick Notes)
  • Get familiar with MoLOS structure before migrating

During Migration​

✅ Migrate Incrementally

  • Don't try to move everything at once
  • Start with critical work (current projects, active tasks)
  • Add historical archives later

✅ Start with Structure

  • Create Areas → Projects → Tasks hierarchy first
  • Organize folder structure for Markdown
  • Map source concepts to MoLOS equivalents

✅ Then Migrate Content

  • Import actual content after structure is ready
  • Upload files in batches
  • Verify each batch before continuing

✅ Keep Both Systems Running

  • Use source tool and MoLOS in parallel during migration
  • Reference source tool while learning MoLOS
  • Don't delete source data yet

✅ Verify Data

  • Check that migrated content is complete
  • Ensure links and references work
  • Confirm tags and categories are preserved

After Migration​

✅ Run Both Systems for 1-2 Weeks

  • Keep source tool for reference
  • Gradually transition work to MoLOS
  • Build confidence in MoLOS workflows

✅ Gradual Transition

  • Move work to MoLOS slowly
  • Adapt your workflow to MoLOS strengths
  • Don't expect 1:1 feature parity

✅ Document Differences

  • Note what MoLOS does better/worse
  • Identify workarounds for missing features
  • Consider building custom modules if needed

✅ Clean Up

  • Once confident, archive source data
  • Keep backup for at least 30 days
  • Delete source accounts if desired

Data Validation Checklist​

Before considering migration complete, verify:

  • All important tasks migrated and visible in MoLOS-Tasks
  • All projects and areas created with correct structure
  • All documents and notes imported to MoLOS-Markdown
  • Links and references working correctly
  • Tags and categories preserved
  • Attachments accessible and linked correctly
  • No data loss detected (compare counts, sample items)
  • Critical workflows tested in MoLOS

Common Questions (FAQ)​

How long does migration take?​

For a typical user with moderate data:

From ToolTime Estimate
Notion → MoLOS30 minutes–2 hours
Obsidian → MoLOS15 minutes–1 hour
Logseq → MoLOS20 minutes–1.5 hours

Time varies based on:

  • Amount of data to migrate (files, tasks, notes)
  • Complexity of your current workflow
  • Familiarity with MoLOS structure
  • Manual vs. automated migration approach

Tip: Start with a test migration of a subset of data to gauge timing.

Will I lose data during migration?​

Risk is minimal if you follow these steps:

  1. ✅ Backup everything before starting
  2. ✅ Keep both systems running during migration
  3. ✅ Verify data after import
  4. ✅ Don't delete source data until confident

MoLOS Data Safety Features:

  • Stores data locally in SQLite database
  • Can backup database file directly
  • Can export data anytime
  • Can restore from backup if needed

Will my formatting be preserved?​

Some formatting changes are expected. This is normal.

✅ Will Be Preserved:

  • Text content and structure
  • Headings and hierarchy
  • Lists (bulleted, numbered, nested)
  • Tables
  • Links and images (if embedded correctly)
  • Tags and categories

⚠️ May Change or Require Cleanup:

  • Rich text styling (custom colors, highlights, fonts)
  • Custom properties and metadata (frontmatter may need manual adjustment)
  • Tool-specific features (Notion embeds, Obsidian plugin content)
  • Complex layouts (Notion columns, etc.)

Can I migrate just some data, not everything?​

Yes! Incremental migration is actually recommended.

Approach 1: Critical Work First

  1. Migrate current projects and tasks (what you're working on now)
  2. Add historical archives later
  3. Import old notes and documentation gradually

Approach 2: Experiment First

  1. Test MoLOS with a small subset of data
  2. Learn the structure and workflows
  3. Do full migration once comfortable

Approach 3: Hybrid Transition

  1. Use both tools in parallel for transition period
  2. Move new work to MoLOS
  3. Keep old work in source tool for reference
  4. Migrate historical data at your own pace

Troubleshooting Migration Issues​

Export Issues​

Issue: "Export from Notion failed or incomplete"

Solutions:

  1. Try exporting smaller batches (one workspace at a time)
  2. Use different export format (Markdown & CSV vs HTML)
  3. Check Notion Status Page for outages
  4. Contact Notion support if issue persists

Issue: "Obsidian vault won't export or plugin conflicts"

Solutions:

  1. Disable all plugins before export
  2. Try copying vault folder directly from file system
  3. Check file permissions on vault directory

Issue: "Logseq export creates empty files or errors"

Solutions:

  1. Try OPML format instead of Markdown (or vice versa)
  2. Close other Logseq graphs before export
  3. Check Logseq version (use latest stable release)

Import Issues​

Issue: "MoLOS won't import files or shows errors"

Solutions:

  1. Check file size — MoLOS has reasonable import limits
  2. Verify file format — should be .md for Markdown
  3. Confirm MoLOS is running
  4. Try importing smaller batches to isolate problematic files

Issue: "Data missing after import"

Solutions:

  1. Verify all files were uploaded (check file counts)
  2. Check MoLOS file permissions
  3. Check available storage space
  4. Re-import missing files individually

Issue: "Formatting looks wrong or broken"

Solutions:

  1. Accept that Markdown is simpler than rich formats
  2. Manually clean up headings and lists
  3. Check for valid Markdown syntax using a linter
  4. Re-create complex content using MoLOS structure

Post-Migration Issues​

Issue: "MoLOS structure doesn't match my workflow"

Solutions:

  1. Adapt your workflow to MoLOS strengths (Areas → Projects → Tasks)
  2. Use MoLOS creatively: Use Areas for broad categories, Projects for specific efforts, Tasks for actionable items
  3. Leverage MoLOS features: Saved views, filters, labels, dependencies
  4. Build custom modules: If you need specific workflows, develop a module

Success Stories​

From Notion to MoLOS: A 30-Day Journey​

User: Jordan Rivera, Full-Stack Developer
Previous Tool: Notion (3 years, 50+ projects, 1000+ tasks)
Migration Duration: 2 hours
Time to Full Adoption: 30 days

Why Jordan Migrated:

"I loved Notion's features, but the cloud-only nature always concerned me. As a developer working with sensitive client data, I needed a local-first solution. MoLOS promised that plus MCP integration for my AI workflows."

Migration Process:

  • Week 1: Migrated active projects and tasks (2 hours)
  • Week 2: Imported historical documentation and notes (3 hours)
  • Week 3: Built custom MoLOS module for client-specific workflow (8 hours)
  • Week 4: Connected AI agents via MCP (30 minutes)

Results After 30 Days:

  • ✅ Productivity: +25% more tasks completed per week
  • ✅ Data Ownership: Full control over data, no cloud concerns
  • ✅ AI Integration: AI agents can now read/write tasks automatically
  • ✅ Cost Savings: $120/month saved (Notion plan cancelled)
  • ✅ Workflow Satisfaction: Jordan says MoLOS structure fits his development workflow better than Notion

Advice from Jordan:

"Don't try to recreate Notion exactly in MoLOS. Adapt your workflow to MoLOS's strengths (Areas → Projects → Tasks). The first week was frustrating, but by week 3 I was more productive than ever in Notion. The MCP integration is a game-changer for my AI-assisted development workflow."

Next Steps After Migration​

Immediate (Day 1)​

  1. Verify All Critical Data

    • Check that all important tasks migrated
    • Confirm documents are accessible
    • Test key workflows (create tasks, access notes)

  2. Test MoLOS Features

    • Explore Areas, Projects, Tasks structure
    • Test Markdown editing and linking
    • Connect AI agents via MCP (if using)

  3. Familiarize Yourself

    • Navigate the interface
    • Customize saved views and filters
    • Adjust settings to your preference

Short-Term (Week 1)​

  1. Get Comfortable

    • Use MoLOS for daily work
    • Learn keyboard shortcuts and UI patterns
    • Experiment with different organizational approaches

  2. Customize for Your Workflow

    • Set up saved views for common queries
    • Create custom labels and tags
    • Configure filters and default views

  3. Learn Advanced Features

    • Explore module documentation
    • Understand MCP integration
    • Learn about custom module development

  4. Join the Community

    • GitHub Discussions for tips and support
    • Share your migration experience
    • Contribute feedback and improvements

Long-Term (Month 1+)​

  1. Build Custom Modules

    • If you have specific workflow needs
    • Develop features missing from source tool
    • Share modules with community

  2. Integrate with Other Tools

    • Connect to calendar, email, or other systems
    • Build automation workflows
    • Leverage MCP for AI integrations

  3. Contribute Back

    • Report bugs and feature requests
    • Improve documentation
    • Share migration scripts or templates

  4. Help Others Migrate

    • Share your success story
    • Contribute migration tips to community
    • Help new users in discussions

Resources​

Documentation​

Community​

Need Help with Migration?

If you encounter issues during migration:

  1. Check this guide — Your issue may be covered in the troubleshooting section
  2. Search GitHub Discussions — Others may have solved your problem
  3. Open an issue — Report bugs or missing features
  4. Join the community — Get help from other MoLOS users

Remember: Migration is a journey, not a race. Take your time, ask for help, and enjoy the benefits of local-first, AI-integrated productivity.

Last Updated: March 21, 2026
MoLOS Version: v1.1.0

Ready to migrate? Start with the Quick Start Guide and come back here when you're ready to import your data.