Why You Can't Just Update Like Normal
If you have a modified Switch running custom firmware, doing a standard system update through the normal settings menu is a surefire way to brick your console. The update process detects the modifications and either fails mid-way or, worse, lets the update go through but then the console can't boot because the firmware and custom firmware versions don't match. This happens constantly. I've seen it happen to people who just sat down and clicked "Update" without thinking about it first. The process requires you to update in a very specific way using specific tools. You need to understand what you're doing, but it's not impossible if you follow the steps exactly. Here's how it actually works in practice. You need the right firmware file for your specific Switch model, the bootloader you're using, and a couple of tools to flash it properly. Let me break down exactly what each piece is and where you get it.
System Firmware File: This is the official Nintendo firmware update, which you can download directly from Nintendo's servers or find on sites like Switch-Mods. You need to match your firmware version to the one you're updating to. If you're currently on 14.1.0 and want to go to 15.0.0, you download the 15.0.0 firmware package. Don't skip this step. Using the wrong firmware version is the most common mistake I see. Bootloader: Depending on your setup, you're likely running either Atmosphere, SX OS, or something similar. Each has different requirements for firmware updates. Atmosphere is the most common, so I'll focus on that. Make sure you have the latest version of your bootloader downloaded before you start. I learned this the hard way once when my bootloader was too old to handle the new firmware, and the console refused to boot into RCM mode after the update. Took me two hours to figure out what was wrong. fusee_gelee payload: This is the tool that lets you enter RCM (Recovery Mode) on your Switch. You need this to run any of the updating tools. Download the latest version from the official Atmosphere GitHub repository.
hactoolnet or similar: This is used to extract and prepare the firmware update files. It's a command-line tool, so if you're not comfortable with terminals, it takes a little getting used to, but there are simpler alternatives if needed.
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The Actual Update Process
Start by backing up your save data and any important files. Use something like JKSV for saves and backup your NAND if you can. I always say this because I've had people come to me after they tried to update and lost everything, and there's nothing I can do for them at that point. A full NAND backup takes about 15 to 20 minutes depending on your SD card speed, so don't skip it. Next, you need to extract the firmware update files. Download the firmware .nca files from Nintendo's servers. The extraction process involves using hactoolnet to pull out the specific firmware files you need. If you're using a pre-packaged firmware update from a trusted source, this step might already be done for you, which is simpler but means you're relying on someone else's preparation. Once your files are ready, you need to enter RCM mode. On a Switch OLED or a Switch V2, you hold volume up and down while inserting the USB-C cable. On older models, it's usually volume up plus power. The exact method depends on your hardware revision. Plug it in, and use TegraRcmGUI or a similar tool to send the fusee_gelee payload to your console.
With the payload running, you can now use tools like KS Installer or Atmosphere's built-in firmware updater. This is where the actual firmware gets written to your console. Follow the instructions for your specific tool carefully. The process itself takes about 5 to 10 minutes. If it takes longer than that, something is wrong and you should stop and investigate.
Common Pitfalls and What to Do About Them
One issue I run into frequently is when people try to update from a very old firmware version to a very new one in a single step. For example, going from 8.1.0 all the way to 15.0.0. This almost never works cleanly. You need to update incrementally, stepping through each major version. It's annoying, but it's the only reliable way. I once tried to skip ahead on a friend's Switch and we ended up with a bootloop that took three hours to fix with a full NAND restore. Another problem is using the wrong payload for your bootloader version. If your Atmosphere is outdated and you send a payload that expects a newer version, the console will either not respond or fail partway through. Always check compatibility between your bootloader and the tools you're using. There's also the issue of SD card file system corruption. If your SD card has any issues, the firmware update can fail silently. I've seen this happen where the update appears to succeed but the console won't boot afterward. Always run a quick check on your SD card before starting. It takes five minutes and can save you hours of troubleshooting later.

After the Update Completes
Once the update finishes, your console should boot normally into the updated firmware. If it doesn't, you likely have a mismatch between your bootloader and the new firmware version. You'll need to go back and update your bootloader first, then retry the firmware update process. If your console is stuck in a bootloop, you'll need to restore from your NAND backup. This is why I emphasized backing up earlier. A restore from backup takes about 20 to 30 minutes depending on your SD card speed, but at least your saves and customizations will be there. Some games and homebrew applications may need to be updated to work with the new firmware version. Check with the developers of any homebrew you use regularly to make sure they support your new firmware version before you go too far into the update process.
When This Method Won't Work
If your Switch has a broken motherboard or a failed eMMC chip, no amount of firmware updating will help. Also, if you're on a firmware version that hasn't been supported by your bootloader yet, you'll need to wait for an update from the bootloader developers. There's no shortcut around that. Sometimes the update process can fail due to power issues. If your console's battery is below 20 percent, the update may abort. Charge it to at least 50 percent before starting. I've lost count of how many times I've seen people try to update with a dead battery and wonder why it doesn't work. The biggest limitation is that this process only works on switches that are already modded. If your switch is completely stock and you've never modded it, this guide doesn't apply to you. You'd need to follow a different set of instructions for that scenario, and attempting to force-mod a stock switch is a much more complex process with higher risk of permanent damage.