Here, we report the results of strain-controlled spin-wave propagation regimes in a double-period multiferroic structure. It consists of an alligator-type magnonic crystal with a period of 250 μm and a piezoelectric layer, featuring a periodic counter-pin-type electrode system with a period of 125 μm. Employing microwave measurements, we acquired the transmission and dispersion of spin waves under various external electric field configurations applied to the piezoelectric layer. The formation of bandgaps in the magnon spectrum and the variation of the spin-wave transmission when altering the configurations of the external electric field are demonstrated. A finite element method reveals that the combination of the non-uniformity in the initial internal magnetic field of the magnonic crystal, which is caused by the presence of periodic alligator-type regions, together with elastic deformations, heightens the amplitude of the modulation of the internal magnetic field. Micromagnetic modeling has demonstrated that this modulation enhancement results in the variation of the spin-wave transmission at the frequency of the magnonic bandgap center of the magnonic crystal. The proposed design of the reconfigurable magnonic crystal creates a condition for the nucleation of the spin-wave bandgap, with further enhancement of the spin-wave reflection from the periodic grating induced by strain. We demonstrate the potential use of the proposed device as a multi-band NAND/NXOR spin-wave based logic gate.