Data protection authorities worldwide have agreed on the value of considering privacy-by-design principles when developing privacy-friendly systems and software. However, on the technical plane, a profusion of privacy-oriented guidelines and approaches coexists, which provides partial solutions to the overall problem and aids engineers during different stages of the system development lifecycle. As a result, engineers find difficult to understand what they should do to make their systems abide by privacy by design, thus hindering the adoption of privacy engineering practices. This paper reviews existing best practices in the analysis and design stages of the system development lifecycle, introduces a systematic methodology for privacy engineering that merges and integrates them, leveraging their best features whilst addressing their weak points, and describes its alignment with current standardization efforts.