How to Troubleshoot High CPU Usage on Linux VPS

A few months ago, one of my websites started loading really slowly. I was hosting it on a Linux VPS, and everything had been fine for weeks. Then, out of nowhere, it felt like the whole server had slowed to a crawl. At first, I thought it was just a traffic spike. But after checking, I saw the CPU usage was almost 100%. Something was wrong.

Have you ever had that happen? Maybe your VPS is lagging. Maybe your website crashes or your SSH session is super slow. These are often signs that your CPU is working too hard.

In this guide, I’ll help you find out why your Linux VPS is using too much CPU. I’ll also show you how to fix it — step by step.

What Is CPU Usage?

Let’s keep it simple.

CPU stands for Central Processing Unit. It’s the brain of your server. It runs your code, handles traffic, and processes everything from commands to website requests.

CPU usage is how much of that brain power is being used.

So if your CPU usage is 90% or more for a long time, your server may feel slow, unresponsive, or even crash.

What Causes High CPU Usage?

There are many possible causes. Here are a few common ones I’ve seen on my own servers:

A program is using too much processing power.
A background process is stuck or looping.
A bad script (like a broken cron job) is running nonstop.
Too many people are visiting your website at once.
Your website is under attack (yes, it happens).
The VPS plan is too small for your needs.

Sometimes it’s a mix of these.

Have you checked your VPS dashboard and seen a red warning or spike in CPU usage? Let’s dig in and figure it out.

Step 1: Log in to Your VPS

First, you need to log in to your server using SSH. If you’re on Windows, use PuTTY. If you’re on Mac or Linux, just use the terminal.

Open your terminal and type:

ssh root@your_server_ip

Replace your_server_ip with your actual server IP address.

If you can’t log in because it’s too slow, try rebooting from your hosting panel (like Vultr, DigitalOcean, or Linode). Then log in right away.

Step 2: Use `top` or `htop` to See What’s Happening

Once you’re logged in, run this command:

top

This will show a live list of processes using your CPU and memory. Look at the %CPU column. The top processes will be listed at the top.

Here’s what to look for:

A process using 80% or more CPU.
The name of the process (like apache2, mysql, php, or python).
How many processes are running at once.

If you see something like php using a lot of CPU, your website or app might be the issue.

Want a better view? Try this:

apt install htop
htop

htop is a more colorful and easy-to-read version of top. It lets you scroll and sort processes better.

Step 3: Stop the Problem Process

Once you know which process is eating the CPU, you can stop it.

Let’s say you see a process with ID 1234 using a lot of CPU. You can stop it like this:

kill -9 1234

But be careful — only kill a process if you’re sure it’s safe. For example, don’t kill a database process unless you know it’s stuck.

If the problem keeps coming back, it’s time to dig deeper.

Step 4: Check Web Server and App Logs

If your server runs websites, the problem might be in your web app.

Check logs here (depending on your web server):

Apache logs:
```
tail -n 50 /var/log/apache2/error.log
```
Nginx logs:
```
tail -n 50 /var/log/nginx/error.log
```
PHP logs:
```
tail -n 50 /var/log/php7.x-fpm.log
```

Look for errors, warnings, or repeated requests.

If you see one IP making thousands of requests per minute, it could be a bot or an attack. That would explain high CPU usage.

Step 5: Check Cron Jobs

Cron jobs are scheduled tasks that run automatically. But sometimes they run too often or get stuck.

To view your cron jobs:

crontab -l

Make sure you don’t have a job running every minute if it takes 5 minutes to complete. That causes overlap and spikes in CPU.

I once had a backup script running every 10 minutes that took 12 minutes to finish. The CPU never got a break.

Step 6: Check for Malware or Bots

Sometimes, the problem isn’t from you. Hackers often try to use your server to mine crypto or send spam.

Here’s what I do to check:

Scan your system:
```
apt install rkhunter
rkhunter --check
```
Check for suspicious processes:
```
ps aux | grep -i miner
```

Also, check if your website is being hit by bots:

tail -f /var/log/nginx/access.log

If you see the same IP making hundreds of requests, block it:

ufw deny from 192.168.1.100

Replace the IP with the one you want to block.

Step 7: Upgrade or Optimize

Sometimes your VPS is just too small. If you’ve tried everything and your CPU is still spiking, consider upgrading your plan.

More CPU cores and more RAM give your apps room to breathe.

Or you can optimize your current setup:

Ways to optimize and lower CPU usage:

Use caching (like Redis or a CDN).
Compress images and files.
Use a lightweight web server (like Nginx).
Limit cron jobs and background tasks.
Use tools like fail2ban to block bad traffic.

Two Quick Lists

Common Reasons for High CPU:

Too many PHP requests
Stuck cron jobs
Bot attacks or scraping
Bad code or infinite loops
Malware or crypto miners
Heavy database queries

Simple Tools That Help:

htop – shows system usage
iotop – checks disk usage
rkhunter – scans for malware
ufw – simple firewall
logwatch – summarizes logs

Wrapping Up

I’ve had days where my whole server slowed down, and I didn’t know why. I’d restart it and hope it would fix itself. But now I know how to check htop, look at logs, and spot trouble before it gets worse.

Have you had a time when your server was slow and you didn’t know what to do?

The more you use these tools, the easier it gets. You don’t need to be a pro to spot high CPU usage. Just log in, look around, and take action.

High CPU usage doesn’t have to be scary. Most problems can be fixed with a few simple steps. And if you ever feel stuck, reach out for help — or just take a break and try again later.

Your Linux VPS will thank you.