In this work, we performed first-principles calculations to study the interactions of Nin clusters (n = 2-5) with graphene. Nin clusters were adsorbed on pristine graphene and graphene with a vacancy. We observed that the adsorption energy is significantly lowered when graphene has a single vacancy. The single vacancy gives place to a charge redistribution that favors chemisorption. The dangling bonds of the carbon atoms produced by the vacancy increase the magnetic moment of the C atoms around the hole induced by the Ni clusters. We found that the situation is very different when the Ni cluster is adsorbed with atoms on both sides of the vacancy. We consider the cases in which one of the Ni atoms is located on one side of the graphene sheet and the rest on the other, Nin,1. The adsorption energy for Ni3,1 and Ni4,1 clusters are slightly larger than when the whole cluster is chemisorbed on one side only, but the charge redistribution, occurring on both sides of the graphene, increases the possibility to adsorb other molecules. For all cases, we analyzed the electronic density of states to account for the electronic changes on the graphene sheet as a function of the size of the Nin cluster. Finally, the Bader effective charges were computed to follow the charge transfer between Nin clusters and the graphene atoms.