Bose-Einstein condensation (BEC) in quantum magnets, where bosonic spin excitations condense into ordered ground states, is a realization of BEC in a thermodynamic limit. Although previous magnetic BEC studies have focused on magnets with small spins of S ≤ 1, larger spin systems potentially possess richer physics because of the multiple excitations on a single site level. Here, we show the evolution of the magnetic phase diagram of S = 3/2 quantum magnet Ba₂CoGe₂O₇ when the averaged interaction J is controlled by a dilution of magnetic sites. By partial substitution of Co with nonmagnetic Zn, the magnetic order dome transforms into a double dome structure, which can be explained by three kinds of magnetic BECs with distinct excitations. Furthermore, we show the importance of the randomness effects induced by the quenched disorder: we discuss the relevance of geometrical percolation and Bose/Mott glass physics near the BEC quantum critical point.