A method for manufacturing a micromechanical system is shown. The method comprises the steps of forming in a front end of line (FEOL) process a transistor in a transistor region. After the FEOL process, a protective layer is deposited in the transistor region, wherein the protective layer comprises an isolating material, e.g. an oxide. A structured sacrificial layer is formed at least in a region which is not the transistor region. Furthermore, a functional layer is formed which is at least partially covering the structured sacrificial layer. After the functional layer is formed removing the sacrificial layer in order to create a cavity between the functional layer and a surface, where the sacrificial layer was deposited on. The protective layer protects the transistor from being damaged especially during etching processes in further processing steps in MOL (middle of line) and BEOL (back end of line) processes. Using an oxide for said protective layer is advantageous, since the same oxide may be used as the basis for a metallization process in the BEOL. Therefore, the protective layer may remain over the transistor and does not need to be removed like the sacrificial layer, which is typically used as a protection for the transistor. Therefore, the protective layer becomes part of the oxide coverage, which is applied before the BEOL process.