We present a proposal for controlling the conversion of ultracold atoms into molecules by fixing the phase difference between two oscillating magnetic fields. The scheme is based on the use of a magnetic Feshbach resonance with a field modulation that incorporates terms oscillating with frequencies corresponding to the main resonance and one of the subharmonics. The interference between the two association processes activated by the oscillating terms is controlled via the phase difference. As a result, significant increase or decrease of the effective interaction strength can be achieved. The realization of the proposal is feasible under standard technical conditions. In particular, the method is found to be robust against the effect of the sources of decoherence present in the practical setup. The applicability of the approach to deal with quadratic terms in the field modulation is discussed.