Manipulation of magnetic ground states by effective control of competing magnetic interactions has led to the finding of many exotic magnetic states. In this direction, the tetragonal Heusler compounds consisting of multiple magnetic sublattices and crystal symmetry favoring chiral Dzyaloshinskii-Moriya interaction (DMI) provide an ideal base to realize non-trivial magnetic structures. Here, we present the observation of a large robust topological Hall effect (THE) in the multi-sublattice Mn$_{2-x}$PtIn Heusler magnets. The topological Hall resistivity, which originates from the non-vanishing real space Berry curvature in the presence of non-zero scalar spin chirality, systematically decreases with decreasing the magnitude of the canting angle of the magnetic moments at different sublattices. With help of first principle calculations, magnetic and neutron diffraction measurements, we establish that the presence of a tunable non-coplanar magnetic structure arising from the competing Heisenberg exchanges and chiral DMI from the D$_{2d}$ symmetry structure is responsible for the observed THE. The robustness of the THE with respect to the degree of non-collinearity adds up a new degree of freedom for designing THE based spintronic devices.