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Linux VPS is considered a safer alternative to Windows servers, but that doesn’t mean the risk of malware infection is zero. Even the most secure systems can be vulnerable if not monitored regularly or if unreliable software is used.

In this article, we’ll explain how to check your Linux VPS for viruses, which tools are best suited for the job, and what to do to avoid future infections. We’ll also share practical tips to help keep your server secure in the long run.

Why You Should Scan Your VPS for Malware

Linux servers are often chosen for their stability, open-source code, and strong community support. But even these servers can:

• Fall victim to rootkits or backdoors
• Become part of a botnet
• Be used for unauthorized cryptocurrency mining
• Send spam or participate in DDoS attacks

Main reasons for infection:

• Unpatched system or CMS vulnerabilities (e.g., outdated WordPress versions)
• Lack of firewall or basic security measures
• Weak passwords or default accounts
• Scripts downloaded from questionable sources

Even if your server seems clean, regularly scanning your VPS is a must, especially if you work with customer data.

Signs Your Linux VPS May Be Infected

Here are some red flags that your system may be compromised:

• Unusual CPU or RAM load
• Suspicious network activity (e.g., constant connections to foreign IPs)
• New user accounts you didn’t create
• Changes in system configs or auto-start settings
• Unknown scripts or executables in /tmp or /var

These are signs that your server needs an urgent scan.

Best Tools to Scan a Linux VPS for Viruses

1. ClamAV — Basic Open-Source Antivirus

One of the most popular antivirus solutions for Linux.

Features:

• Scans system files and directories
• Supports scheduled scans via cron
• Signature database updates with freshclam

Install on Ubuntu:

sudo apt update  

sudo apt install clamav clamav-daemon  

sudo freshclam

Scan:

clamscan -r /home

You can also schedule weekly automatic scans.

2. Chkrootkit — Rootkit Scanner

This tool specializes in detecting hidden threats that may evade typical antivirus tools.

Install:

sudo apt install chkrootkit

Scan:

sudo chkrootkit

Results appear in the terminal — look for lines marked “INFECTED.”

3. Lynis — Security Auditing Tool

More than just antivirus — Lynis is a full-blown security auditor for system configurations.

Benefits:

• Assesses your system’s security level
• Reviews SSH, sudo, and cron settings
• Provides tips to enhance protection

Install:

sudo apt install lynis

Audit:

sudo lynis audit system

4. Rkhunter — In-Depth Rootkit Detection

Another powerful rootkit scanner with different detection methods and more customization.

Install and run:

sudo apt install rkhunter  

sudo rkhunter –update  

sudo rkhunter –check

Add it to cron for daily scans.

Extra Linux VPS Security Tips

Keep your system up to date — apt update && apt upgrade

Configure a firewall — use ufw or iptables to block unwanted ports

Change the default SSH port and disable password login

Use SSL certificates to encrypt traffic — this secures your websites. You can order one at server.ua

Make regular backups — best automated

Monitor resource usage — tools like htop, iftop, vnstat can help

Disable root SSH access, use sudo

What to Do If You Find Malware on Your Server

1. Isolate the VPS — shut down all connections except SSH (or temporarily disable networking)
2. Remove infected files — manually or with antivirus tools
3. Check all cron jobs and startup scripts (~/.bashrc, ~/.profile, systemd units)
4. Change all passwords: root, sudo, control panels, FTP, etc.
5. Reinstall the VPS if you’re unsure the threat is fully removed
6. Restore from a clean backup, if available

Who Should Regularly Audit Their VPS?

• Developers hosting apps on Linux servers
• Companies renting VPS to handle customer data
• Online business owners who value stability and reputation

At Server.ua, you can rent a VPS with pre-configured security tools, backups, and 24/7 support.

For colocating your own hardware, check out our colocation service in a professional data center.

Conclusion

Linux VPS security isn’t a one-time setup — it’s an ongoing process. Regular antivirus scans, system updates, firewall configuration, and backups should become your routine.

With simple tools like ClamAV, Lynis, and Rkhunter, you can catch threats early and avoid major damage.

Work with a reliable provider like Server.ua, and your VPS will be both high-performing and 100% secure.