From Chaos to Clarity: My Multi-Vault Approach to Obsidian Knowledge Management

A comprehensive guide to organizing multiple types of Obsidian vaults for improved performance and workflow

Why Multiple Vaults

When I first began using Obsidian, I maintained a single vault for everything—personal notes, research materials, reference documents, and more. However, as my digital library grew, I noticed significant slowdowns in startup times and occasional freezing. This experience led me to rethink my approach to vault management.

The primary reasons I now use multiple vaults are twofold. First, I needed to separate my own thoughts from external content. This aligns perfectly with the Zettelkasten method's recommendation to distinguish between your ideas and reference materials. Second, I wanted to optimize the performance of my main vault that contains my most important personal notes. By distributing content across purpose-specific vaults, I've achieved faster startup times, eliminated freezing issues, and significantly improved my note-taking and editing experience.

This distinction between personal and external content is an important one. In my note-taking system, I categorize notes as:

• Fleeting Notes: Quick, temporary notes that might be my own thoughts or content from external sources

• Permanent Notes: My personal insights, written in my own words and fully processed

• Literature Notes: My summaries and reflections on other people's content, but written in my own words

The key insight here is that when we process external content through our own understanding (like with Literature Notes), it deepens our comprehension—similar to the Feynman learning technique where explaining a concept to someone else strengthens your grasp of it.

My Vault Ecosystem

My current setup includes over 10,000 notes in my primary vault, which contains mostly my own thoughts. Meanwhile, my reference vault houses over 10,000 items, including reading annotations, podcast transcriptions and other lengthy external content. If all this were combined in a single vault, the sheer volume would severely impact performance. By maintaining separate vaults, I can focus on processing my own ideas rather than getting bogged down with external information.

Primary Personal Vaults

My main ecosystem consists of desktop and mobile vaults containing predominantly my own thoughts and notes.

On desktop, I maintain two key vaults:

• Work Life: This serves as my primary repository for scientific research, personal development, projects, and daily insights. It's where I spend most of my time and contains all my critical content—work-related materials, life planning, developmental thinking, and project tasks.

• Work Extra: This secondary vault stores archived materials and less important content like tool usage notes. When I complete tasks in my main vault and archive them, they often move here. It helps keep my main vault uncluttered while preserving potentially useful information. Think of it as a digital attic—less frequented but still valuable for occasional reference.

On mobile, I use:

• Obsidian Mobile: This vault primarily captures ideas when I'm away from my computer. I've designed it for quick thought capture rather than extensive research. For example, when attending events where I need to record temporary thoughts, I'll capture them here first and later sync them to my desktop vaults. I regularly sync important content from here to my desktop vaults. As I mentioned in a previous article, I use buffer folders to prioritize organizing important content first, while less critical notes can wait for processing.

Temporary Vaults

Sometimes specific circumstances require dedicated spaces:

• Vault Temp: I created this when working temporarily at another company. It allowed me to bring only the necessary notes for that specific context without exposing my entire personal vault on a temporary work computer. Rather than synchronizing my entire knowledge base to a corporate device, I could selectively bring over only what was needed for the temporary assignment. Once the assignment ended, I transferred relevant notes back to my main vault. This approach proved invaluable for maintaining privacy while still having access to essential information during my temporary assignment.

Reading and Reference Vaults

For managing external content, I maintain separate vaults:

• Reading Annotation: This vault contains highlights and notes synchronized from Readwise, Hypothesis, and similar services. It's a hybrid space containing external text alongside my annotations. I also store podcast transcriptions here from shows I frequently listen to. When I encounter valuable podcast content, I save the transcription for later reference. This separation ensures my primary vault focuses on my processed thoughts rather than raw highlights.

• Reference File: This vault exclusively stores other people's content, including web clippings (e.g., via Obsidian Clipper or MarkDownload), AI tool conversations (ChatGPT, Perplexity, etc.), and exported Markdown files. I've tested various AI chatbots including ChatGPT and Perplexity, and found that exporting conversations as Markdown creates an excellent reference library. While these conversations include my prompts, the majority of the content is externally generated, which is why I store them separately from my personal notes.

While Obsidian can handle PDFs and has third-party plugins for reference management, I prefer using specialized tools like Zotero for academic references. The specialized extensions for PDF reading, annotation, translation, and Obsidian synchronization make it a more professional solution for reference management. For miscellaneous PDFs from project work, I use DEVONthink and similar tools rather than cluttering my Obsidian vaults. Though I might elaborate on reference management strategies in a future article, my current approach leverages external tools while maintaining links to my Obsidian notes.

A key principle I follow: use specialized tools for specialized tasks. This makes my workflow both simpler and more efficient.

Special Purpose Vaults

I also maintain vaults for specific functions:

• Obsidian Publish: A dedicated vault for my PTKM website content. If you're interested in more of my thoughts on knowledge management, consider visiting the site.

• Tool Test: Where I experiment with new plugins before adding them to my main vault. This has been invaluable for testing the 11 Obsidian plugins I've developed without risking stability issues in my primary workspace. I also use BRAT to test plugins that haven't yet been officially released to the Obsidian marketplace. Testing in a separate vault has often revealed that while some plugins seemed interesting initially, they didn't actually fit into my established workflow. This pre-testing approach prevents me from bloating my main vault with unnecessary plugins that might impact performance.

Linking Between Vaults

The true power of a multi-vault system emerges when you can seamlessly connect information across these separated spaces. Vault setups aren't static—notes often need to move between vaults at different stages of their lifecycle. For instance, notes from a temporary vault may need to be transferred to my main vault once their specific purpose is complete.

Additionally, sometimes I don't need to permanently transfer notes but simply need to temporarily access content from another vault. For example, when shopping or attending meetings, I might need to reference notes from my desktop vault on my mobile device if I can't access my computer.

Linking Methods

There are powerful tools for connecting notes across vaults:

• Advanced URI and Obsidian URI: These allow me to link specific notes across vaults and even to external applications. I frequently link notes and tasks to external tools like Calendar and Todoist reminders. For example, I often add Advanced URI links to calendar event descriptions. The calendar event serves as a reminder, but I can click the link to access more detailed notes in Obsidian. This approach allows me to keep my detailed content in one central location while making it accessible from wherever I need it.

• External Tools: I use Hookmark on macOS to create versatile connections between different content types, while DEVONthink helps me index multiple libraries simultaneously. With DEVONthink's indexing capabilities, I can manage notes from different Obsidian vaults as if they were in a single library—enabling unified search and linking, which is particularly powerful.

For example, I've integrated Obsidian with Todoist using my own plugin called Todoist Context Bridge. This allows me to sync tasks between systems while keeping detailed context in Obsidian. While I might have thousands of tasks in Obsidian, only 100-200 critical ones get synchronized to Todoist for active monitoring. This selective synchronization ensures I'm not overwhelmed by my complete task database while still maintaining access to all the contextual details within Obsidian.

The Todoist Context Bridge plugin serves a specific purpose in my workflow: before I mark a task as complete in Todoist, it can synchronize any descriptions or notes I've added back to Obsidian. This creates a feedback loop where quick notes captured in my task manager find their way back to my knowledge management system for further processing, referencing, and linking to related notes.

Similarly, when writing in tools like Ulysses, I link back to specific Obsidian notes containing research and inspiration. This creates a seamless workflow where my detailed notes remain in Obsidian while other tools serve as focused interfaces for specific purposes. When I hit writer's block, I can quickly jump to my Obsidian notes to review related ideas and inspirations.

Transferring Notes Between Vaults

For actual content migration, I use several methods:

• Creating symbolic links (for instance, my daily notes folder is shared between mobile and desktop vaults)

• Hazel automation for moving notes between specific folders

• Manual transfers via the file system, which can be tedious but sometimes necessary (especially for hidden folders like the plugins directory that aren't accessible within Obsidian itself)

• The Vault Transfer plugin (though I use this less frequently now)

One particularly useful setup is the symbolic link I've created between my mobile and desktop vaults to share daily notes. This allows content recorded in either location to be instantly accessible from all my devices and vaults without any manual intervention. My Periodic Notes folder (containing daily, weekly, and monthly notes) is shared between devices, which has been transformative for my daily note-taking, as I no longer need to worry about synchronization issues between devices—notes captured on my phone immediately appear in my desktop environment, and vice versa.

I also use Hazel (and similar tools on other operating systems) to automate file movement between vaults. For example, when I record ideas on my mobile device, sync them to my computer, and then process them, Hazel can automatically move them to the appropriate folder in my main vault. This automation works for moving files to any location—inside or outside Obsidian vaults—making it incredibly efficient.

Synchronization and Backup Strategies

Different vaults serve different purposes, so they require tailored synchronization approaches. My guiding principle is to determine the synchronization and backup strategy based on the specific purpose of each vault:

• Is real-time synchronization needed across multiple devices?

• Is the focus more on backup than synchronization?

• Does the vault contain primarily Markdown notes or other formats?

• Is it storing my personal notes or reference materials from others?

Synchronization Methods

• Obsidian Sync: I use this for vaults requiring real-time updates across devices. My current plan supports synchronizing 10 vaults, which covers my essential needs. The immediacy of this solution makes it perfect for my most-used vaults where I need instant access to information across devices. A key advantage is the encryption feature, which keeps private content secure. Having used Obsidian for five years now, I've found this service invaluable for my workflow.

• Cloud Storage: For reference materials that don't need immediate syncing, I use iCloud. This functions more as a backup than true synchronization. For example, my Reference File vault is synchronized this way since I primarily access it from my desktop and don't have a strong need for mobile access. My phone is primarily for capturing my own thoughts rather than browsing reference materials. When choosing cloud storage, I consider encryption and privacy features, especially for sensitive personal information.

• Git: For content I plan to make public (like my PTKM website), Git provides excellent version control while allowing me to exclude sensitive information. I specifically use this for backing up content that's already intended to be public, avoiding the privacy concerns that would come with storing strictly personal notes in an unencrypted repository. For my PTKM website, I use a three-pronged approach: Obsidian Publish for managing and publishing, Git for backup and version control, and Obsidian Sync for multi-device editing capabilities.

Different vaults might benefit from different synchronization strategies. For instance, my PTKM website vault is synchronized using all three methods mentioned above, while my Reference File vault only uses iCloud because real-time synchronization is less critical for reference materials.

Backup Approaches

Beyond synchronization, I employ multiple backup strategies:

• Obsidian's built-in File Recovery with customized intervals and retention periods

• Cloud storage backups

• Time Machine for system-level protection

I don't back up everything with the same rigor—test vaults receive minimal backup attention, while my main research vault gets comprehensive protection. This prioritization ensures my critical knowledge assets are well-protected without wasting resources on easily replaceable content. For instance, my Plugin Test vault doesn't contain irreplaceable information, so I don't prioritize backing it up.

Maintaining Consistency Across Vaults

To reduce cognitive load, I maintain similar folder structures across my vaults whenever possible. This enhances note retrieval efficiency and makes navigation intuitive regardless of which vault I'm using. In fact, whether I'm working with Obsidian vaults, Zotero reference libraries, or even general file organization on my computer, maintaining consistent structures dramatically reduces the mental effort required to find information.

I also establish consistent plugin configurations and keyboard shortcuts by copying relevant settings between vaults. Many configurations are one-time setups that can be easily transferred to new vaults. For example, I might copy the entire plugin folder to another vault, or transfer keyboard shortcut settings files. The Obsidian forum has discussions about sharing configurations between vaults, though I haven't needed to dive deeply into those resources.

However, I don't aim for perfect uniformity. Different vaults serve different purposes and therefore benefit from customized setups. For instance, my reference vault only needs basic URI generation capabilities, while my main vault requires a full suite of productivity enhancements. I prioritize consistency in the aspects that matter most for my workflow while allowing for purpose-specific customizations.

My approach is incremental and needs-based. Instead of trying to configure everything at once, I address specific needs as they arise. For example, my Task Marker plugin was initially only used in my desktop vault, but when I realized I needed the same functionality on mobile to mark important content with appropriate task statuses, I simply copied the plugin folder to my mobile vault.

It's important to recognize that vault setups evolve organically. When I first started using Obsidian, I had only one vault (my current main vault). Over time, as it accumulated more content—including reference materials and miscellaneous items—I decided to split it into separate vaults for highlights and less important content. Later, I created a mobile-focused vault, and eventually a temporary vault for my company exchange work. Each of these developments was driven by emerging needs rather than planned in advance.

Balance and Perspective

Always remember why you're setting up different vaults in the first place. The ultimate goal is to support your knowledge system and task management—not to create extra work for yourself. Constantly reflect on whether you're spending too much time configuring your vaults at the expense of your actual projects and goals.

Avoid perfectionism, as it's impossible to achieve a perfect setup in one go, especially when your needs and understanding will change over time. Make incremental improvements based on actual needs rather than hypothetical ideals. Even if you update settings in one vault, there's no need to propagate those changes to all your other vaults immediately—doing so with every change would consume too much time and energy.

Setting up multiple vaults is itself a complex project involving many steps and tasks that might take considerable time. Manage this setup process alongside your other tasks, and remember that vault configuration should serve your projects and goals—not the other way around.

Conclusions

The multi-vault approach has transformed my Obsidian experience from overwhelming to optimized. By thoughtfully distributing content based on purpose and origin, I've created a system that balances performance with accessibility.

This strategy does require some initial setup time, but the long-term benefits in terms of speed, stability, and mental clarity have proven well worth the investment. Whether you're managing thousands of notes or just beginning your Obsidian journey, considering a deliberate vault structure might significantly enhance your knowledge management experience.

The flexibility to adapt this system as needs change remains one of its greatest strengths. As my work evolves, so too can my vault organization—always optimizing for the perfect balance between connection and separation in my digital thinking space.

Through thoughtful division of my digital library into focused vaults, I've not only improved technical performance but also achieved greater mental clarity. Each vault serves a specific purpose, helping me maintain clear boundaries between different types of information while preserving powerful connections across my entire knowledge system.

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