We report here the observation of the inverse exchange bias phenomenon in the ferrimagnetic doubleperovskite Gd₂CoRuO₆. The compound crystallizes in a monoclinic structure (space group P2₁/n), and it undergoes long-range magnetic ordering below TC = 60 K. The ferrimagnetic state of the sample is manifested through magnetization reversal at low temperature. In order to corroborate the role of local structure on the magnetic properties of Gd₂CoRuO₆, we have performed a combined magnetization and x-ray absorption spectroscopy study on two different samples prepared through different cooling protocols (slow cooling and furnace cooling). Extended x-ray absorption fine-structure analysis indicates the presence of strong antisite disorder between Co and Ru in both samples. However, the slow-cooled sample shows completely random antisite disorder, whereas, small Co- and Ru-rich patches appear in the furnace-cooled sample. In both samples, a significant amount of mixed valency in Co and Ru ions is evident from our x-ray absorption near-edge structure. The antiparallel ordering along with different temperature dependence of the three magnetic sublattices, Gd, Co, and Ru, can be responsible for negative magnetization, whereas the inverse exchange bias effect can be attributed to the mixed interfacial coupling between adjacent magnetic nanoclusters. The difference in local structure can nicely be accounted for by the observed variations of the magnetic properties between two samples of Gd₂CoRuO₆.