In magnetic trilayer systems, spin pumping is generally addressed as a reciprocal mechanism characterized by one unique spin mixing conductance common to both interfaces. However, this assumption is questionable in cases where different types of interfaces are present in the material. Here, we present a general theory for analyzing spin pumping in cases with more than one unique interface. The theory is applied to analyze layer-resolved ferromagnetic resonance experiments on the trilayer system Ni$_{20}$Fe$_{80}$/Ru/Fe$_{49}$Co$_{49}$V$_2$ where the Ru spacer thickness is varied to tune the indirect exchange coupling. The results show that the spin pumping in trilayer systems with dissimilar magnetic layers is non-reciprocal, with a surprisingly large difference between spin-pumping induced damping of different interfaces. Our findings have importance on dynamics of spintronic devices based on magnetic multilayer materials.