The rise of large-scale quantum computing poses a significant threat to traditional cryptographic security measures. Quantum attacks undermine current asymmetric cryptographic algorithms, rendering them ineffective. Even symmetric key cryptography is vulnerable, albeit to a lesser extent, suggesting longer keys or extended hash functions for security. Thus, current cryptographic solutions are inadequate against emerging quantum threats. Organizations must transition to quantum-safe environments with robust continuity plans and meticulous risk management. This study explores the challenges of migrating to quantum-safe cryptographic states, introducing a comprehensive security risk assessment framework. We propose a security risk assessment framework that examines vulnerabilities across algorithms, certificates, and protocols throughout the migration process (pre-migration, during migration, post-migration). We link these vulnerabilities to the STRIDE threat model to assess their impact and likelihood. Then, we discuss practical mitigation strategies for critical components like algorithms, public key infrastructures, and protocols. Our study not only identifies potential attacks and vulnerabilities at each layer and migration stage but also suggests possible countermeasures and alternatives to enhance system resilience, empowering organizations to construct a secure infrastructure for the quantum era. Through these efforts, we establish the foundation for enduring security in networked systems amid the challenges of the quantum era.