We present dataset of Co nanoparticles production using a Multiple Ion Cluster Source (MICS). We study the evolution of the mean size and deposition rate of Co nanoparticles as a function of the power and argon flux applied to the Co magnetron, the aggregation length of the Co magnetron and the total argon flux. The results show the strong influence of these parameters on the mean size of the nanoparticles and the efficiency of the process as well as on the atomic deposition rate. In particular, it is shown that nanoparticles of mean size ranging from 4 to 14 nm can be produced and that the influence of the working parameters on the production of magnetic nanoparticles is more complex than for the case of noble metal presented previously.