Should I Use The M.2 Heatsink With My Mobo (Or A Separate One?)

M.2 storage drives offer you the best performance, but they also generate some of the highest temperatures on your motherboard. More motherboard manufacturers are shipping with M.2 heatsinks, but are they worth it?

The M.2 heatsink that comes with your motherboard is a great option if you’re looking to save money and ensure that all of your components fit. However, these heatsinks typically offer less heat mitigation than aftermarket or custom options. A custom M.2 heatsink will give you the best heat mitigation, and it won’t add too much extra cost to your build.

Here’s why you shouldn’t sweat the heat mitigation options for your M.2 drives.

If A Motherboard Has a Built-in M.2 Heatsink, Should You Use It?

A motherboard with bare M.2 slot and also a separate M.2 heatsink cover
A motherboard with bare M.2 slot and also a separate M.2 heatsink cover.

Built-in M.2 heatsinks are a great place to start. They are great for cost savings and the convenience of coming with your motherboard. More and more motherboards are starting to come with their own M.2 heatsinks and this is giving PC builders an important advantage.

There is one quick thing we should talk about before we get started. Even a bad heatsink is better than no heatsink. The heatsink that comes with your motherboard might not be the best quality, but it’s still going to offer some mitigation when compared to nothing at all.

The worst case scenario is that the heatsink that comes with your motherboard is going to function as a stopgap solution. This is something that will buy you time and help protect your PC building investment while you upgrade to a high-end heatsink.

Built-in M.2 Heatsinks Save You Money

The single biggest advantage of a built-in M.2 heatsink is that it’s going to save you a lot of money. Building a PC is already pretty expensive and picking up a motherboard that comes with its own heat mitigation is just going to save you some aftermarket costs.

However, you’ll still need to do some research to figure out exactly what these cost-savings look like. A motherboard that comes with a low quality M.2 heatsink won’t be saving you any money if you wind up burning out your M.2 drive just to save a few bucks on an upgraded heatsink.

A Built-in M.2 Heatsink Also Fits Your Motherboard

Another important advantage is that the M.2 heatsink that comes with your motherboard is designed to fit.

This is a big problem that we see all the time with beginner PC builders and veterans alike. Making sure that all of your components fit on your motherboard and in your PC case is often a pretty big challenge. Once everything is plugged into your motherboard, those heatsinks often wind up making or breaking your overall fit – especially since they can be double or triple the height of an M.2 drive without a heatsink.

The heatsink that comes with your motherboard is much more likely to fit than an aftermarket option. You’ll have less guesswork, measuring, and worrying when you stick with the heatsink that’s built to fit your motherboard.

When Built-in M.2 Heatsinks Aren’t The Right Choice

Two M.2 NVMe drives installed in an Asus B550 Plus motherboard
Two M.2 NVMe drives with aftermarket heatsinks.

Then again, there are some pretty compelling reasons to ditch the heatsink that came with your motherboard and pick up an upgraded aftermarket model.

At the end of the day, your heatsink has one job. It’s there to mitigate the high temperatures that come with M.2 drives and protect the money you spent building your PC.

Think about it this way: Would you rather leave several hundred dollars sitting outside on your lawn or inside your house protected in a safe? Heat mitigation is all about protecting the time and money you put into building your PC. So, why not always get the best?

Poor Quality

We hinted at this earlier, but it’s worth giving its own focus. The heatsink that comes with your motherboard isn’t always the best quality. These heatsinks are usually functional, but when it comes to performance we tend to want something a little bit higher than just “functional.”

This is especially the case for M.2 drives. These drives can get incredibly hot and they’re often connected right next to graphics cards and other PCIe devices that crank up the heat. This is one area of PC building where you really don’t want to skip on heat mitigation.

Heatsinks Built Into The Wrong Slots

A GEN4 M.2 SSD means that it supports a PCIE 4.0 slot in the motherboard
A GEN4 (PCIe 4) M.2 drive

The companies that manufacture motherboards are also making some pretty strange choices when it comes to which slots they build their heatsinks into.

We see a lot of motherboard companies building their heatsinks into their PCIe 3 slots, not the PCIe 4 slots. This might make sense given how common PCIe 3 drives are, but it doesn’t make sense when we consider that a PCIe 4 slot can run a PCIe 3 drive.

Then we have to talk about the heat. An M.2 drive in a PCIe 4 slot is going to generate a ton of heat. The performance that you got with the latest iteration of technology also means that you’re going to be generating a lot of excess heat in your drives.

This is why heat mitigation is so important for PCIe 4 M.2 drives. You’ll be protecting your M.2 drive, your motherboard, and also the other drives that are nearby that could be taking heat damage from an M.2 drive that isn’t properly mitigated.

What About M.2 Drives With Their Own Heatsinks?

You can also find M.2 drives that come with their own heatsinks.

This is typically a high-end feature for performance M.2 drives. These heatsinks can be shipped as part of the drive itself like the WD_BLACK SN850 1TB PCIe 4 M.2 drive, or they can be a separate component that you have the option of attaching during installation.

Note: you will notice that the “built-in” heatsinks that ship directly with an M.2 drive can sometimes be a lot more expensive than buying an aftermarket heatsink. When I purchased two M.2 drives, the “with heatsink” option cost around 60% more – so I gave this a miss. But if the “with heatsink” option is only $30-40 more, it’s probably worth buying it.

These heatsinks have some advantages over the ones that come with your motherboard, but they also have one major drawback that we need to consider.

Higher Performance

These heatsinks typically offer much higher performance. The manufacturers of M.2 drives often ship their products with heatsinks that are designed to handle the thermal output of these high-end storage drives.

This means that you’re going to get heat mitigation that goes above and beyond what comes with your motherboard. This is significant in that it protects your drive, but it’s also protecting the other devices plugged into your motherboard. The more you keep your PC temperature down, the more longevity you’re going to get out of your components.

Problems With Fit

There is a big downside to these heatsinks. They’re built to fit a wide range of motherboards and layouts, but this means that they might not fit your specific situation.

This is the one size fits all problem. It’s not that these heatsinks fit every motherboard, it’s that they fit most motherboards. This means that your particular motherboard, combination of drives, or the other heat mitigation options you’re using might cause fit issues with these M.2 drives. The Western Digital drive we mentioned earlier is fairly bulky and might not work in every PC layout.

So, are there any alternatives to using these manufacturer included heatsinks?

Aftermarket M.2 Heatsinks—Pros and Cons

Various parts of a third party M.2 NVMe SSD heatsink
Various parts of a third party M.2 NVMe SSD heatsink

Welcome to the world of aftermarket and two heatsinks. These tend to offer the highest possible heat mitigation while also being fully customizable to fit not only your motherboard, but the specific layout of other components that you’ve chosen.

Let’s take a look at the pros and cons of these custom-made heat mitigation options.


To be honest, the pros of aftermarket heatsinks for M.2 drives far outstrip the cons.

  • The biggest pro is that you’re going to get the best possible heat mitigation for these high temperature drives. You won’t have to waste your time and money with included heatsinks that often cut corners when it comes to construction. You might pay a premium, but you’ll get the highest build quality with the best materials.
  • We also have to talk about style. Building a PC is typically mostly about performance, but we’d be kidding ourselves if it isn’t also about making a machine that looks amazing. You can find custom M.2 heatsinks that feature LED lights, your favorite colors, or that match the overall style and tone of your PC.
  • There are also custom M.2 heatsinks that go above and beyond for call of duty. These heatsinks can even feature multiple levels of heat mitigation designed to handle an M.2 drive in a PCIe 4 slot.


An M.2 PCIE4 SSD with a third party heatsink attached to it
An M.2 PCIE4 SSD with a third party heatsink attached to it

They’re only really two cons and these can be easily controlled.

  • The first is that these aftermarket heatsinks do represent an additional cost. The good news is that these costs typically aren’t too high and are fairly easy to manage. This is especially the case when compared with the cost of an M.2 drive itself.
  • The next thing we have to consider are issues of fit. You need to do some careful measuring to make sure that these heat mitigation options fit the layout of your motherboard. This shouldn’t be much of an issue, but it will mean spending a little extra time making some careful measurements to ensure that the heatsinks that you purchase fit your motherboard.
cropped A picture of me Tristan
About Tristan Perry

Tristan has been interested in computer hardware and software since he was 10 years old. He has built loads of computers over the years, along with installing, modifying and writing software (he's a backend software developer 'by trade').

Tristan also has an academic background in technology (in Math and Computer Science), so he enjoys drilling into the deeper aspects of technology.

Tristan is also an avid PC gamer, with FFX and Rocket League being his favorite games.

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2 thoughts on “Should I Use The M.2 Heatsink With My Mobo (Or A Separate One?)”

  1. If I got an M.2 Drive with its own heatsink, is there any problem if the motherboard features a heatsink for this type of drive also?

    • There’s no issue using both heatsinks no (it probably is ideal to use both, in a perfect world). However sometimes the extra height of the M.2 drive (with heatsink) means that you can’t use the motherboard’s one too – meaning you then have to choose between the M.2’s heatsink and the motherboard one (which is what I found with my Asus B550M-Plus motherboard). I ended up using the M.2’s heatsink, instead of the motherboard one. But if you can use both, that won’t be an issue at all 🙂


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