Post-Quantum Cryptography: Preparing Your Certificate Infrastructure for the Next Threat

The conversation around Post-Quantum Cryptography (PQC) has officially moved from academic theory to operational reality. For years, the threat of a quantum computer capable of breaking our current en...

Tim Henrich
November 25, 2025
9 min read
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Post-Quantum Cryptography: Preparing Your Certificate Infrastructure for the Next Threat

The conversation around Post-Quantum Cryptography (PQC) has officially moved from academic theory to operational reality. For years, the threat of a quantum computer capable of breaking our current encryption standards felt like a distant, science-fiction problem. But with the National Institute of Standards and Technology (NIST) on the verge of publishing its final PQC standards in 2024, the starting gun for migration has been fired.

The most immediate danger isn't that a powerful quantum computer will appear overnight and break your live TLS sessions. The real, present-day threat is "Harvest Now, Decrypt Later" (HNDL). Adversaries are already capturing and storing vast amounts of encrypted data today, betting that they can decrypt it in the future once a cryptographically relevant quantum computer (CRQC) is available. Any data that needs to remain secure for the next 5-10 years—customer PII, intellectual property, financial records, state secrets—is already at risk.

This isn't just about swapping out an algorithm. It's a fundamental shift in our Public Key Infrastructure (PKI) that will touch every certificate, every server, and every application. For DevOps engineers, security professionals, and IT administrators, the time to prepare is now. This guide provides a practical playbook for making your certificate infrastructure quantum-resistant.

The Core Challenge: Why PQC is Different

The transition to PQC isn't as simple as upgrading from SHA-1 to SHA-2. The new quantum-resistant algorithms, while brilliant, come with significant practical trade-offs. The most notable difference is the size of the public keys and signatures they produce.

Compared to the lean and efficient Elliptic Curve Cryptography (ECC) we rely on today, the leading PQC candidates are orders of magnitude larger. Let's look at a comparison between ECDSA using the P-256 curve and CRYSTALS-Dilithium3, one of the primary algorithms selected by NIST for digital signatures.

Metric ECDSA (P-256) CRYSTALS-Dilithium3 Impact
Public Key Size ~65 bytes ~1,952 bytes (1.9 KB) ~30x larger
Signature Size ~70 bytes ~3,293 bytes (3.3 KB) ~47x larger

This size increase has cascading effects on your infrastructure:

  • Bloated Certificates: X.509 certificates will become significantly larger, as they must contain these larger public keys and be signed with larger signatures.
  • Performance Overhead: Larger certificates and signatures mean more data must be transmitted during a TLS handshake, potentially increasing latency for web applications.
  • Protocol and Hardware Limits: Some protocols and resource-constrained devices (like IoT sensors or smart cards) have strict limits on payload size that may be exceeded by PQC data.

Failing to account for these changes can lead to broken applications, failed TLS handshakes, and unforeseen performance bottlenecks.

The Strategy: Crypto-Agility and Hybrid Certificates

A "rip and replace" approach to PQC is impossible and dangerous. The global PKI is too vast and interconnected to switch overnight. The industry has therefore coalesced around a two-pronged strategy: crypto-agility and hybrid implementation.

1. Achieving Crypto-Agility

Crypto-agility is the ability of a system to switch between cryptographic algorithms without requiring a full software rewrite and redeployment. For decades, many systems have hardcoded algorithms directly into their source code (e.g., SHA256withRSA). This is a technical debt that makes migration incredibly painful.

Best Practice: Abstract your cryptography. Instead of hardcoding algorithms, pull them from configuration files. This allows you to update your cryptographic standards by changing a config value and restarting a service, rather than undertaking a full development cycle.

2. The Hybrid Certificate Approach

To ensure a smooth transition and maintain backward compatibility, the de facto standard is the hybrid certificate. A hybrid certificate contains two sets of public keys and signatures: one classical (like ECDSA) and one post-quantum (like Dilithium).

Here’s how it works:
1. Generation: A Certificate Authority (CA) issues a single X.509 certificate that embeds both an ECDSA public key and a Dilithium public key. It is then signed with both the CA's classical private key and its PQC private key.
2. Validation:
* A legacy client that only understands ECDSA will see and validate the classical signature, ignoring the PQC data it doesn't recognize. The connection succeeds.
* A modern, PQC-aware client will validate both the ECDSA and Dilithium signatures. Both must be valid for the connection to be trusted.

This approach provides the best of both worlds: quantum resistance for those who can support it and uninterrupted service for those who can't. Security is maintained because an attacker would need to break both the classical and quantum algorithms to forge a connection.

Your PQC Migration Playbook: A 4-Step Guide

Moving from awareness to action is critical. Here is a practical, step-by-step plan to begin preparing your certificate infrastructure today.

Step 1: Discover and Inventory Your Cryptographic Assets

You cannot migrate what you cannot see. The first and most crucial step is to create a comprehensive inventory of every certificate in your environment. This goes beyond just public-facing web server certificates. You need to find:

  • Public TLS/SSL certificates from CAs like Let's Encrypt or DigiCert.
  • Internal certificates used for microservices, databases, and internal APIs.
  • Code signing certificates used in your CI/CD pipelines.
  • SSH keys, API keys, and other cryptographic secrets.
  • The cryptographic libraries (e.g., OpenSSL, BoringSSL) and hardware security modules (HSMs) in use.

Manually tracking this across a modern enterprise is impossible. This is where automated certificate lifecycle management and monitoring tools are essential. A platform like Expiring.at provides the visibility you need, automatically discovering certificates across your networks, cloud accounts, and Kubernetes clusters. Knowing the location, owner, and expiration date of every certificate is the foundational data for your PQC migration plan.

Step 2: Analyze and Prioritize

Once you have your inventory, you can begin prioritizing. Not all systems are created equal. Group your applications and services into tiers based on risk and technical readiness.

  • High Priority: Systems protecting data with a long security lifespan. This includes customer databases, financial transaction systems, and source code repositories. These are prime targets for "Harvest Now, Decrypt Later" attacks.
  • Medium Priority: Systems with high visibility or critical operational roles, but with data that has a shorter lifespan.
  • Low Priority: Systems with ephemeral data or those that are easier to update, such as internal staging environments.

Also, assess the technical debt. Is an application using a modern crypto library like OpenSSL 3.x, or is it running on a legacy system with hardcoded algorithms? The latter will require significantly more lead time to remediate.

Step 3: Test in a Lab Environment

Before you touch production, build a lab environment to gain hands-on experience with PQC algorithms. Modern versions of OpenSSL (3.0 and newer) include experimental support for several of the NIST-selected algorithms.

Let's walk through generating a hybrid Certificate Signing Request (CSR) using OpenSSL. This CSR will contain both a standard secp384r1 (ECC) key and a dilithium3 (PQC) key.

1. Generate the Classical Key

First, create a standard Elliptic Curve private key.

# Generate an ECC private key using the secp384r1 curve
openssl genpkey -algorithm ec -pkeyopt ec_paramgen_curve:secp384r1 -out classical_key.pem

2. Generate the Post-Quantum Key

Next, generate a private key for the Dilithium algorithm. Note that PQC algorithms may need to be explicitly enabled in your OpenSSL configuration.

# Generate a CRYSTALS-Dilithium3 private key
# This requires a PQC-enabled build of OpenSSL
openssl genpkey -algorithm dilithium3 -out pqc_key.pem

3. Create a Hybrid Certificate Signing Request (CSR)

Now, we'll create a single CSR that requests a certificate for both keys. The -new flag indicates we're creating a new request, and we provide both private keys with the -key option. OpenSSL is smart enough to combine them.

# Create a CSR with two public keys
openssl req -new \
    -key classical_key.pem \
    -key pqc_key.pem \
    -out hybrid_csr.pem \
    -subj "/C=US/ST=California/L=Mountain View/O=My PQC-Ready Org/CN=pqc-test.example.com"

You can inspect the resulting CSR to see that it contains information for both algorithms.

# Inspect the contents of the hybrid CSR
openssl req -in hybrid_csr.pem -text -noout

This hands-on testing is invaluable. It will help your team understand the new workflows, identify gaps in your tooling, and measure the performance impact of the larger key sizes in a controlled environment.

Step 4: Engage Your Ecosystem and Automate

PQC migration is not a solo effort. You must engage with your technology partners to understand their roadmaps and readiness.

  • Certificate Authorities (CAs): Major CAs like DigiCert and others are already offering PQC test certificates. Talk to your provider about their plans for issuing production-ready hybrid certificates.
  • Hardware Security Modules (HSMs): If you use HSMs to protect your private keys, confirm that your vendor has a firmware update planned to support the new algorithms. The computational intensity of PQC algorithms may require hardware upgrades.
  • Cloud Providers: Ask your cloud provider (AWS, Azure, GCP) about their timeline for supporting PQC in their managed services, such as load balancers, VPNs, and KMS.
  • Automation: Review your certificate automation scripts. If you use ACME clients like certbot to manage Let's Encrypt certificates, monitor their projects for announcements about PQC support. Your deployment and management tools must be updated to handle the new hybrid formats.

Conclusion: Start Today for a Secure Tomorrow

The transition to Post-Quantum Cryptography is one of the most significant security upgrades the internet has ever undertaken. It is a marathon, not a sprint, and the organizations that start preparing now will be the most resilient.

The path forward is clear:
1. Inventory Everything: Build a complete, real-time inventory of all your cryptographic assets. You cannot secure what you do not know you have.
2. Embrace Crypto-Agility: Eradicate hardcoded algorithms from your codebase and move to a configuration-driven approach.
3. Plan for Hybrid: Base your migration strategy on the hybrid certificate model to ensure security and backward compatibility.
4. Test, Test, Test: Start experimenting with PQC algorithms in a lab environment now to build institutional knowledge and uncover potential roadblocks.

The quantum threat is no longer theoretical. By taking these deliberate, practical steps today, you can build a certificate infrastructure that is robust, agile, and ready for the quantum future.

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