While certification is widely recognized as a means to increase system trustworthiness and reduce uncertainty in decision making, it faces severe challenges preventing a wider adoption thereof. Certification is not adequately planned and integrated within the development process, leading to suboptimal scenarios where certification introduces the need to further modify the developed system with high costs. We propose a methodology that bridges the gap between software development and certification processes. Our methodology automatically produces the certification requirements driving all steps of the development process, and maximizes the strength of certificates while taking costs under control. We formalize the above problem as a multi-objective mathematical program and solve it through a genetic algorithm. The proposed approach is tested in a real-world, cloud-based financial scenario at CaixaBank and its performance and quality is evaluated in a simulated scenario.