Microparticles of Ni45.7Mn36.6In13.5Co4.2 have been prepared by means of different grinding methods (hand-grinding, cryo-milling, planetary ball-milling) followed by annealing treatments in order to recover the original martensitic transition and magnetic properties. A rapid reduction of particle size down to the micrometers has been obtained after few hours of milling, as it results from morphological analyses. Milling temperature, time, and medium strongly impact on the degree of induced stresses and particles aggregation, significantly changing the morphology, crystal structure and magnetic properties. It was found that both magnetic and magneto-structural phase transitions can be recovered by high-temperature annealing treatments (T > 1000 K). Time and temperature of the treatment have been optimized in relation to the disorder introduced by the milling process, which depends on its energy and duration. In general, our results show the strong dependence of the magneto-structural properties of the NiMnInCo compound on microstructural features, atomic order and chemical homogeneity, that imposes a careful selection and improvement of the preparation route.