Zóbel married Trinidad de Ayala (1856-1918) on February 5, 1875. The couple took a whirlwind honeymoon trip to Japan, San Francisco, the World’s Fair of 1876, and Europe, where their children were born. The couple decided to live briefly in Spain after Jacobo decided to study transportation systems in Europe, and he renewed his numismatic research, publishing a major work entitled "Estudio Histórico de la Moneda Antigua Española Desde Su Origen Hasta El Imperio Romano" in 1878.