We report on the study of the non-trivial Berry phase in superconducting multiterminal quantum dots biased at commensurate voltages. Starting with the time-periodic Bogoliubov-de Gennes equations, we obtain a tight binding model in the Floquet space, and we solve these equations in the semiclassical limit. We observe that the parameter space defined by the contact transparencies and quartet phase splits into two components with a non-trivial Berry phase. We use the Bohr-Sommerfeld quantization to calculate the Berry phase. We find that if the quantum dot level sits at zero energy, then the Berry phase takes the values $varphi_B=0$ or $varphi_B=pi$. We demonstrate that this non-trivial Berry phase can be observed by tunneling spectroscopy in the Floquet spectra. Consequently, the Floquet-Wannier-Stark ladder spectra of superconducting multiterminal quantum dots are shifted by half-a-period if $varphi_B=pi$. Our numerical calculations based on Keldysh Greens functions show that this Berry phase spectral shift can be observed from the quantum dot tunneling density of states.