We present a scalable method for the fabrication of site-controlled quantum dots (QDs) embedded in optical resonators. The position of the quantum dots is determined by nucleating their growth in an array of nano-holes that is aligned to a set of markers, allowing the precise overlay of the resonator geometry over the QD array. Coupling of the QDs to the resonators is demonstrated by the resonant enhancement of the spontaneous emission observed in photoluminescence experiments.