Securing Linux Servers: Top Strategies To Ensure Safe Systems

In early 2024, Linux surpassed a 4% share of the global desktop operating system market, reinforcing its growing adoption across enterprises. However, as Linux systems gain traction, cyber threats targeting them are also on the rise. Securing Linux servers is no longer just an option—it’s a necessity to safeguard sensitive data and ensure compliance.

Basic security measures alone are not enough to defend against today’s evolving cyber threats. To strengthen your defenses, here are advanced security strategies to secure your Linux environment, mitigate risks, and maintain a resilient infrastructure.

Why is Linux security important?

As Linux continues to power enterprise servers, cloud environments and critical infrastructure, ensuring its security is more crucial than ever. While Linux is known for its stability and robust security features, it is not immune to cyber threats. Attackers exploit misconfigurations, unpatched vulnerabilities and weak access controls to gain unauthorized access or deploy malware.

A well-secured Linux environment protects sensitive data, maintains system integrity,and ensures compliance with industry regulations. Without proper security measures, organizations risk operational downtime due to cyberattacks.

To mitigate these risks, businesses rely on advanced security solutions and best practices. Proactive monitoring and patch management solutions ensure vulnerabilities are addressed before they can be exploited.

By understanding the importance of Linux security, organizations can take proactive steps to fortify their infrastructure and defend against emerging threats.

Top strategies for ensuring a secure Linux server

Securing a Linux server requires a proactive approach, as cyber threats continue to evolve. While Linux is known for its security and stability, improper configurations, outdated software, and weak access controls can leave systems vulnerable to attacks. A well-secured Linux server not only protects sensitive data but also ensures compliance with industry regulations and prevents operational disruptions.

Below are key strategies to secure a Linux server, enhance its resilience and defend against potential threats.

Stay up to date

One of the most critical security measures for Linux servers is keeping all software up to date. Outdated packages and unpatched vulnerabilities provide an easy entry point for attackers, making regular updates essential for system security.

• Enable automatic updates where possible to ensure that security patches are applied as soon as they become available.
• Use package managers to manually check for updates.
• Regularly update the Linux kernel, as it includes crucial security patches and performance improvements.
• Subscribe to Linux security mailing lists and monitor official security advisories for potential vulnerabilities.

By staying up to date with the latest patches and security fixes, organizations can minimize risks and ensure a more secure Linux server environment.

Implement (and maintain) a firewall

Firewalls are the first major line of defense for secure Linux distros. Firewalls monitor traffic that comes in and out of a network. If incoming traffic doesn’t fit certain criteria, the firewall can quickly block it and protect against viruses, denial-of-service (DoS) attacks and other malware before it causes damage. 

To keep your company safe, you can choose hardware firewalls or software firewalls (or both) for your Linux server security. Hardware firewalls are their own physical devices. They protect entire enterprise networks. While they are certainly an investment, both in terms of money and in setup time, they have distinct advantages. Because they’re separate devices, they don’t take up CPU or memory capacity and can be managed externally. On the other hand, firewall security for Linux environments are typically installed on individual machines. Software firewalls are better suited for workstations and individual servers because they have more configurability. 

Firewalls are important, but you can’t just turn them on and forget them; they must be maintained. You need to follow best practices for managing firewall rules for your firewall to be effective. Protect your Linux servers by regularly updating and auditing firewall rules. Be sure to establish audit trails, test firewall rules thoroughly before you apply them, and frequently back up your firewall configuration.

Firewall maintenance and best practices involve a lot of work. The good news, though, is that a lot of that work can be automated. You can use automated tools to scan for vulnerabilities and automatically backup configurations. Automating rule analysis is also helpful. You can also set your stateful firewalls to automatically manage connection states, reducing the need to open unnecessary ports. Some helpful tools for automating tasks are iptables, nftables, ufw and firewalld.

Use an SSH key pair

Using SSH key authentication instead of passwords significantly enhances the security of remote server access. Unlike passwords, which can be guessed or brute-forced, SSH keys use a cryptographic key pair for authentication, making unauthorized access much harder.

• Generate a public-private key pair using ssh-keygen and store the private key securely.
• Disable password-based authentication (PasswordAuthentication no) in the SSH configuration file.
• Store the public key on the server for secure authentication.
• Use passphrase-protected SSH keys for an extra layer of security in case the private key is compromised.

By implementing SSH key-based authentication, you can secure remote access and protect your Linux server from brute-force attacks.

Make privileged user accounts

Instead of using a single root account for administrative tasks, creating privileged user accounts with least privilege access minimizes security risks.

• Use sudo to grant elevated privileges to specific users rather than providing full root access.
• Apply the principle of least privilege (PoLP)—each user should only have the permissions necessary for their tasks.
• Regularly audit and remove inactive or unnecessary privileged accounts to prevent security loopholes.
• Use sudo logs to monitor privileged activity and detect unauthorized commands.

Restricting administrative access to privileged user accounts reduces the risk of system-wide compromise and enhances Linux security.

Use 2FA

Two-Factor Authentication (2FA) adds an extra security layer by requiring a second form of verification beyond just a password. Even if an attacker steals a password, they would still need the second authentication factor to gain access.

• Enable 2FA for SSH logins using tools like Google Authenticator or pam_duo.
• Use time-based one-time passwords (TOTP) for authentication.
• Require 2FA for sudo privileges to secure privileged actions.

Implementing 2FA prevents unauthorized access and adds a strong layer of protection for securing Linux servers.

Only use necessary hardware

Minimizing the attack surface includes removing or disabling unused hardware and peripherals that could introduce vulnerabilities.

• Disable USB ports if external devices are not required, preventing unauthorized data transfers or malware injection.
• Remove unused network interfaces to reduce potential attack vectors.
• Avoid running unnecessary peripheral services like Bluetooth or audio drivers on production servers.
• Implement device control policies to prevent unauthorized hardware from being connected.

By reducing unnecessary hardware usage, organizations can eliminate security risks and enhance Linux server security.

Disable root access

Allowing direct root login is a major security risk, as it gives full administrative control to anyone who gains access. Disabling root access forces users to log in as non-root users and use sudo for administrative tasks.

• Set PermitRootLogin no to disable root login via SSH.
• Enforce strong passwords or SSH key authentication for all users.
• Use sudo to grant limited, controlled access to necessary administrative tasks.

Disabling root access minimizes security risks and ensures that only authorized users can perform critical system actions.

Check and close open ports

Open ports expose services to potential attacks, so regularly auditing them and closing unnecessary ones is essential.

• Use netstat -tulnp or ss -tulnp to list open ports and their associated services.
• Block unused ports using firewall rules (iptables, nftables, or firewalld).
• Implement port scanning tools like nmap to identify unnecessary exposure.
• Restrict external access to critical services like SSH, MySQL, or PostgreSQL.

By checking and closing open ports, you reduce the risk of unauthorized access and strengthen Linux security.

Use IDS for protection from internal threats

Firewalls are great at detecting and defending against external threats. However, your Linux servers could be vulnerable to internal threats as well. That’s where Intrusion Detection Systems (IDS) come in. IDSs can detect suspicious activity from internal users and alert network administrators in real time. IDSs can also log the event so admins can understand better where the attack came from, how it affected the network and how to prevent it from happening again. 

Network-based IDSs typically analyze network packets and provide a broader view of an entire network. If suspicious activity occurs, network-based IDSs (or NIDS) can alert admins and block the threat in real time. Companies may also benefit from host-based IDSs (or HIDS). These systems typically have deeper details into threats, but they only provide post-event analysis, so you don’t get real-time information. Combining IDSs of either type with other security measures create a layered defense for a secure Linux server.

Make use of automation

Automating security tasks helps ensure consistent protection for Linux servers while reducing the risk of human error. Security automation tools can streamline patch management, vulnerability scanning, and compliance monitoring.

• Use configuration management tools like Ansible, Puppet, or Chef to automate security settings and system hardening.
• Implement automated patching tools.
• Set up log monitoring automation with tools like ELK Stack (Elasticsearch, Logstash, Kibana) or Splunk to detect security anomalies in real time.
• Automate firewall rules and access controls to prevent unauthorized changes.

By leveraging automation, organizations can enhance security, improve response times, and reduce manual workload while ensuring their Linux servers remain secure.

Continuously monitor server logs and activities

Regularly monitoring server logs and system activities is crucial for detecting security threats, identifying suspicious behavior, and ensuring compliance with security policies. Log analysis helps in early detection of intrusions, misconfigurations, and anomalies.

• Use built-in Linux tools like journalctl, syslog, and logwatch to track system logs.
• Deploy Security Information and Event Management (SIEM) tools such as Graylog, Splunk, or Wazuh for centralized log analysis.
• Enable real-time alerting for unusual activities, such as repeated failed login attempts or unauthorized file changes.
• Monitor SSH access logs to detect brute-force attacks.

Continuous log monitoring strengthens Linux security by helping administrators detect and respond to threats proactively.

Conduct regular security audits

Performing regular security audits ensures that Linux servers remain protected against evolving threats. A structured audit helps identify vulnerabilities, misconfigurations, and compliance gaps before they can be exploited.

• Use Lynis or OpenSCAP for automated security assessments and compliance checks.
• Perform vulnerability scanning with tools.
• Review file and directory permissions to ensure that only authorized users have access.
• Conduct penetration testing periodically to simulate real-world attack scenarios and evaluate server security.

Regular security audits help maintain a strong defense against cyber threats, ensuring that Linux servers remain secure, compliant, and resilient.

How to secure Linux confidently with SUSE

Selecting the right operating system for your Linux workloads has a major impact on the security of your environment. SUSE Linux is a highly reliable, scalable and secure server operating systems family. SUSE Linux provides a secure foundation for your Linux infrastructure. SUSE Linux Enterprise Server comes with advanced security features like AppArmor for application-level security and comprehensive patch management to make sure your workloads are secure and compliant. Even better, SUSE offers long-term support to make sure you maintain security and compliance long after your purchase has been made. 

You can configure your SUSE Linux in enforcing mode for maximum security. Since SUSE Linux Enterprise Server is highly customizable, you can also tailor it for your specific use cases to ensure your security is as unique as your data.

Securing Linux with SUSE: Taking your server security to the next level

Keeping your Linux enterprise server secure requires constant work and vigilance. Fortunately, by following the best practices discussed in this article, you can stay ahead of cyber threats. The more proactive you are about server security, the safer your company will be. These tips for advanced Linux security will help keep your firewall security robust and your data safe. 

To learn more about a Linux enterprise server with a robust security posture, check out SUSE Linux Enterprise Server.  

FAQs on securing Linux

What is security-enhanced Linux?

Security-Enhanced Linux (SELinux) is a security architecture for Linux systems that enforces mandatory access controls (MAC) to restrict system interactions and prevent unauthorized access. Developed by the NSA, SELinux provides an extra layer of security by defining and enforcing policies that limit what applications and users can do, reducing the risk of exploits.

What is Linux hardening?

Linux hardening refers to the process of strengthening a Linux system’s security by applying best practices and configurations to minimize vulnerabilities. This includes keeping software updated, using firewalls, disabling unused services, enforcing strong authentication methods, and implementing access controls to protect against cyber threats.

Is Linux secure?

Yes, Linux is considered highly secure, but like any operating system, it requires proper configuration and maintenance. By default, Linux offers strong user privilege management, open-source transparency, and a security-focused design, but regular updates, firewalls, and access controls are essential to prevent attacks and ensure system integrity.