Modern database systems are critical for storing sensitive information but are increasingly targeted by cyber threats, including SQL injection (SQLi) attacks. This research proposes a robust security framework leveraging Docker-based virtualisation to enhance database security and mitigate the impact of SQLi attacks. A controlled experimental methodology evaluated the framework’s effectiveness using Damn Vulnerable Web Application (DVWA) and Acunetix databases. The findings reveal that Docker significantly reduces the vulnerability to SQLi attacks by isolating database instances, thereby safeguarding user data and system integrity. While Docker introduces a significant increase in CPU utilisation during high-traffic scenarios, the trade-off ensures enhanced security and reliability for real-world applications. This study highlights Docker’s potential as a practical solution for addressing evolving database security challenges in distributed and cloud environments.