In 2002, after spells at clubs in his native state, Baptista joined his father's staff at Goiás, as a fitness coach. The duo remained together for the following nine years, only splitting due to the Japanese tsunami in 2011, when both were at Kashiwa Reysol; Eduardo subsequently returned to Sport (club which he already worked from 2007 to 2009) while Nelsinho remained at Kashiwa.