Silica is the main component of the Earth's crust and is also of great relevance in many branches of materials science and technology. Its phase diagram is rather intricate and exhibits many different crystalline phases. The reported propensity to amorphization and the strong influence on the outcome of the initial structure and of the pressurization protocol indicate the presence of metastability and large kinetic barriers. As a consequence, theory is also faced with great difficulties and our understanding of the complex transformation mechanisms is still very sketchy despite a large number of simulations. Here, we introduce a substantial improvement of the metadynamics method, which finally brings simulations in close agreement with experiments. We unveil the subtle and non-intuitive stepwise mechanism of the pressure-induced transformation of fourfold-coordinated alpha-quartz into sixfold-coordinated stishovite at room temperature. We also predict that on compression fourfold-coordinated coesite will transform into the post-stishovite alpha-PbO2-type phase. The new method is far more efficient than previous methods, and for the first time the study of complex structural phase transitions with many intermediates is within the reach of molecular dynamics simulations. This insight will help in designing new experimental protocols capable of steering the system towards the desired transition.