The ISC International Journal of Information Security

Abstract The rapid advancement of quantum computing poses a direct threat to classical public-key cryptographic systems at the core of Internet security protocols. Post-quantum cryptography (PQC) has therefore become central to ongoing standardisation and early deployment efforts. This paper presents a comparative analysis of PQC integration into TLS, SSH, and IPsec, examining cross-cutting challenges, protocol-specific trade-offs, and deployment considerations. Our findings show that PQC adoption introduces markedly uneven overheads across protocols: handshake latency may increase by up to 600% in TLS, by 29% in SSH, and by up to 300% in IPsec, while memory requirements in hybrid configurations can exceed 300 KB in resource-constrained environments. We further demonstrate that message fragmentation, certificate chain expansion, and cumulative rekeying costs emerge as protocol-dependent bottlenecks, underscoring that migration strategies must be tailored to the architecture and operational context of each protocol. Beyond performance, we identify interoperability gaps, downgrade vulnerabilities, and side-channel risks as critical obstacles to secure deployment. By combining empirical performance evidence with a structured review of challenges and deployment strategies, our study provides actionable insights for practitioners, informs ongoing standards development, and highlights research priorities essential to building a resilient, quantum-resistant Internet infrastructure.