Why SSH Key Management Matters in Modern Security

The Secure Shell (SSH) protocol is a secure method for accessing remote systems and devices, authentication, and encryption.

While SSH uses public-key cryptography, it traditionally operates independently of Public Key Infrastructure (PKI) unless extended with certificate-based authentication mechanisms. PKI can help organizations manage digital and machine identities through SSH certificates that authenticate users and devices for critical tasks like automated backups, file transfers, remote server administration, and DevOps workflows.

With the rising number of remote, cloud-based technologies and architectures, SSH keys are vital to secure access in automated environments. 

SSH keys are generally considered safer than passwords for these administrative and automated tasks. They feature public-private key cryptography and are often significantly longer than passwords, making them far more difficult to brute force. 

However, cyber threats are only increasing in sophistication, highlighting common SSH key vulnerabilities like unauthorized duplication and poor lifecycle management. To truly secure machine and digital identities, organizations must move beyond manual SSH key management.

The problem with SSH keys

SSH keys are critical digital identities used for secure remote access, file transfers, and automated workflows. However, they pose significant challenges in security and governance. The main challenges with keys include:

• No defined lifecycle: Unlike certificates, keys do not expire by default and lack built-in mechanisms for revocation or renewal, making them prone to long-term sprawl and misuse. If an attacker gains control of a key that was used decades ago and never decommissioned, they could still gain the same level of system access.
• Decentralized management: SSH private keys are stored locally on devices. If private keys are not secured, they’re susceptible to copying, replication, and unauthorized use, especially for privileged access.
• Limited visibility: Most organizations lack comprehensive insight into where their keys are stored and how they are used. This gap enables key sprawl and creates opportunities for malicious insiders or mismanaged deployments to exploit unmanaged keys.
• Manual monitoring burdens: Many teams still rely on ad hoc, manual procedures to discover, rotate, and revoke keys. This approach does not scale in modern environments and often leads to operational blind spots. 

If these challenges aren’t addressed, unmanaged SSH identities introduce significant risks to your digital trust environment, undermining the integrity of machine and user authentication processes.

The risk is even higher for SSH keys that had root or administrator access, as they can act as a backdoor allowing attackers to issue themselves new, trusted keys your organization doesn’t know about.

How Keyfactor Automates SSH Key Management

SSH certificates (SSH certs) address the inherent risks of SSH keys by introducing lifecycle automation and built-in expiration dates, minimizing long-term key sprawl and enforcing regular rotation.

However, it’s still vital for businesses to perform comprehensive certificate discovery to build a complete inventory of all certificates. Just like keys, companies without a full understanding of their certificate inventory (usually due to manual certificate management) assume a lot of risk if those unknown certificates are misused.

The benefits of SSH certificates and lifecycle automation include:

• A centralized trust model where SSH certs rely on a certificate authority (CA) to sign and validate identities. This replaces the decentralized nature of keys and unifies trust decisions under one authority. 
• Enhanced auditing and reporting through standardized metadata attached to each identity, which supports visibility, compliance, and governance across your infrastructure. Certificates’ enhanced metadata capabilities also allow for more granular, conditional access policies.
• Scalability and automation, because SSH certs integrate easily with automation and centralized security solutions, reducing manual errors and aligning with modern DevOps workflows. With increased cloud reliance and interconnected architecture, the ability to scale and automate certificate management keeps certificates from expiring or providing unauthorized access.
• Reduced theft risk as the standardized rotation windows of SSH certs keeps certificates fresh, helping your business ensure governance and reduce the risks of private key compromise.

Keyfactor’s mission is to secure all machine and digital identities, positioning SSH identity management, whether through keys or certificates, as a vital component of your broader digital trust strategy.

Keyfactor Command’s SSH Key Manager module helps organizations still using keys by centralizing discovery, monitoring, and rotation. This helps identify and close any potential security gaps in your keys. Meanwhile, Keyfactor’s EJBCA platform also supports SSH certificate automation.

Best Practices for SSH Key Security and Access Control

Access controls and policies will boost the overall security of your PKI and therefore your organization. On top of using tools like Command or EJBCA to secure SSH keys or replace them with SSH certs, we recommend you:

• Enforce least privilege access by assigning only the minimal level of SSH access required for each user or device. This ensures only the admins directly responsible for configuration and changes that impact your architecture have the access to do so.
• Implement role-based access control (RBAC) and limit SSH access by IP address or user group.
• Disable direct root login via SSH. Instead, leverage sudo privileges for admin tasks.
• Document SSH identity management policies, including lifecycle guidelines for key and certificate creation, approval, expiration, and revocation. Include policies for responding to potential unauthorized access and other cyber threats.
• Ensure that access policies align with ISO 27001 and other regulatory frameworks focused on securing sensitive data and digital identities.

Monitor and audit

You can only ensure your policies and controls are securing your organization by monitoring and auditing SSH activity.

• Enable comprehensive logging of SSH access attempts, capturing which identities (keys or certs) are used, when, and from where. If any access attempts occur outside their normal usage, flag the access for immediate review and potential revocation of the key.
• Centralize log collection with tools like syslog, Splunk, or ELK Stack to detect and respond to suspicious SSH activity.
• Establish alerts for unusual SSH activity, like logins during off-hours, from new IPs, or with newly provisioned identities.
• Regularly review authorized keys and certificates files to confirm that only approved identities remain in use and to retire unused or unauthorized identities.
• Use automated identity tracking to locate stale, inactive, or orphaned SSH identities, ensuring consistent rotation and decommissioning.

Advanced SSH Identity Security

As threats evolve, so do the methods you should use to protect your SSH identities. We recommend you: 

• Encrypt private SSH keys with strong passphrases to guard against brute-force attacks. Passphrases over 14 characters are generally considered strong.
• Securely cache decrypted keys during a session to balance usability and security. Keys should never be left “in the open” while decrypted.
• Use hardware-backed identity storage (like YubiKeys, TPMs, or smart cards) to generate and protect SSH private keys in a non-exportable form. These keys can then be used to request and authenticate with SSH certificates. Along with biometrics, hardware-backed identity storage tools make it significantly more difficult for attackers to exploit keys or certificates.
• Enforce policies that limit SSH authentication to hardware-backed or ephemeral SSH identities, especially for privileged accounts and sensitive environments.

Modern SSH Identity Security Starts with Automation

For large enterprises managing thousands, or tens of thousands, of identities and associated SSH keys and certificates, manual SSH key management is simply not scalable. It’s easy to lose track of or fail to revoke keys, putting your organization at risk and also keeping your security teams responding to rogue keys rather than more proactive security measures.

Organizations should prioritize moving from SSH keys to SSH certificates to ensure secure, lifecycle-controlled SSH access. Automation and centralized trust models, like those enabled by Keyfactor Command and EJBCA, are critical to securing digital identities and maintaining compliance in a modern IT landscape.

Treat SSH identity management as a core element of your digital trust and machine identity security strategy. Implement advanced SSH key and identity security policies, and automate with trusted tools where possible.

Would you like to take control of your SSH key security? Use Keyfactor Command to automate key rotation, enforcement, and lifecycle management without the manual hassle. Get all of your questions answered here.