E-commerce Security is a part of the Information Security framework and is specifically applied to the components that affect E-commerce that include Computer Security, Data security and other wider areas of the Information Security framework. E-commerce security has its own particular touch and is one of the highest visible security components that affect the end user through their daily payment interaction with business. E-commerce security is the protection of E-commerce assets from unauthorized access, use, alteration, or destruction. Dimensions of E-commerce security-Integrity, Non-repudiation, Authenticity, Confidentiality, Privacy, Availability has been discussed. E-Commerce offers the banking industry great opportunity, but also creates a set of new risks and vulnerability such as security threats. Information security, therefore, is an essential management and technical requirement for any efficient and effective Payment transaction activities over the internet. Still, its definition is a complex Endeavour due to the constant technological and business change and requires a coordinated match of algorithm and technical solutions. In this paper, the proposed methodology for E-commerce security has been discussed, various reasons of vulnerabilities arising in the Security of E-commerce, Different security issues in E-commerce and proposed methodology using AES algorithm for prevention against SQL injections, Price manipulation, weak authentication and authorization, cross site scripting.