Building a second brain is supposed to make things easier, but for me it became a way to avoid using my first one. What ended up happening is that I spent more time building and maintaining these productivity systems than actually doing my work. Each tool also has its own structure that you need to adapt to, so when you’re juggling multiple tools, your work becomes fragmented. Of course, there’s also the issue of outsourcing my thinking.

The more I leaned on these tools, the less I engaged my own brain. And the solution isn’t to abandon the tools entirely, but rather just rethink how I use them. So I’ve been more intentional with setups that support my thinking rather than dictate it. Before I get into how I’ve adjusted my approach, it helps to look at exactly why these setups can backfire, and how “second brain” type of tools can actually be worse for productivity if you rely on them too much.

Each “second brain” tool has its own model

So you start organizing things to fit the tool’s structure

Every second brain app comes with its own model for organizing information and that structure ends up shaping how you work. For example, building a second brain in AFFiNE made me adapt to its block-based structure, and NotebookLM forced me to find a workaround to its limited note-taking tools. All your notes, tasks, references, and everything else need to fit into the app’s architecture, so you adapt your working and thinking styles to the tool instead of the other way around.

Even apps that seem flexible have rules around simple things like tagging and linking, so you start making organizational decisions based on those rules instead of what the work actually needs. This can create a subtle but persistent pressure to conform to the tool’s logic, which can slow down decision-making and derail the structure of your work. For example, I’ve been duplicating notes and forcing tags just so links and searches work properly in an app, instead of letting my content itself guide how I interact with it.

Fragmentation across tools

When you rely on more than one second brain tool

Relying on more than one second brain type of tool introduces another layer of disconnect. Every app has its own terminology and organization system, which means information rarely flows seamlessly between them. Not to mention, it makes it that much easier to outsource your thinking because every corner you turn, there are a bunch of tools making decisions for you.

You end up thinking less about your work and more about how to manage a million tools and all the integrations between them. This is not a good use of time and effort, in my opinion.

Optimization for capture over input

Collecting and organizing everything, but doing so little

One of the things I love about second brain tools is that many of them are designed for capturing information quickly. For example, all you have to do to get your sources into NotebookLM is click a button once via a browser extension. The problem with this is that it encourages hoarding notes and links without actually processing or using them.

Over time, this focus on input over application creates a passive habit. The more I capture content, the less I engage my brain to actually work with the materials. It’s good to have some type of system to store your resources and ideas, but a great system is the one that keeps you coming back to engage with the work.

Treating static information as authoritative

When stored knowledge misleads

Second brain tools are built to store knowledge, but not all stored information stays accurate or useful over time - what once made sense can become irrelevant today. The more structured a system feels, the more your brain can assume the information is correct, even in cases when it’s not. AI tools and automated summaries can make this worse by presenting old, outdated notes and research as if they’re still valid.

Without actively revisiting and revising old content, it’s easy to start treating your archive as authoritative rather than provisional. And relying on it too heavily means you’re outsourcing judgment to something static, and in my case, this has guided my decisions in the wrong direction at times.

Putting my first brain back to work

Using the tools without handing over thinking

Second brains are great for storing and retrieving information, but I was also trying to outsource my thinking to it. I was reaching for notes before trying to remember things on my own, checking my productivity setups before forming my own opinions, and deferring judgment to AI summaries instead of practicing it myself. It's not the tools' fault; they were just performing the way they were designed to, but I’ve been using them as a substitute for thinking rather than support for it.

The easiest way I changed this approach was by using good ol’ pen and paper for my notes, ideas, and rough sketches - it actively engages the brain. And then it was just a matter of being more intentional about which, and how many, second brain tools I use. One PKM app for curated knowledge, and one AI tool for augmentation (not decision-making). Personally, I prefer AFFiNE and NotebookLM, along with my local plain text stack. Now that my setup is simpler, my brain does the deciding, and the tools only step in once there’s something worth storing or checking.

Building a second brain is great, but only if you do it for the right reasons

Second brain tools and systems are undoubtedly useful, but if you're not intentional about how you use them, they can quickly start replacing original thinking and judgment. It's easier to start relying on notes and summaries than to actively reason through problems yourself and engage with content on your own terms.