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- Unpatched system or CMS vulnerabilities (e.g., outdated WordPress versions)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
- Isolate the VPS — shut down all connections except SSH (or temporarily disable networking)
- Remove infected files — manually or with antivirus tools
- Check all cron jobs and startup scripts (~/.bashrc, ~/.profile, systemd units)
- Change all passwords: root, sudo, control panels, FTP, etc.
- Reinstall the VPS if you’re unsure the threat is fully removed
- 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.
