The increasing complexity of software systems along with expanding connectivity has necessitated the evolution of an integrated security framework adopting innovative techniques for secure software systems. This paper proposes a layered security architecture for threat management using a multi-agent system to meet the above objective. Layer- 1 of this framework is designed for elicitation of realistic and flawless security requirements. Layer-2 uses a Multi-Agent system planning for avoidance of threats optimally. In this mechanism autonomous agents interact and coordinate with each other to achieve the common goal of software security. An adaptive defense mechanism using Meta-Agents in multi-agent system in conjunction with fuzzy logic to counter the adaptive and compound threats is the responsibility of Layer-3. Guidelines proposed in this paper have augmented this security architecture as a two-fold defensive strategy to ensure that a hacker is not able to tamper data even if they penetrate the periphery defenses. These proactive steps can be implemented during the design and development phases of the software life cycle in an incremental way as per the budget and security requirements of a software project. A case study on internet banking is included in the paper to describe the proposed security framework.