The aim of our study was to determine if two protocols of (−)-epicatechin (Epi) (short and long) can modify fat, muscle and bone mass, in the male offspring of the maternal rat obesity model induced by high-fat diet (HFD). Four male offspring per group from different litters were randomly selected to the control or Epi intervention groups. We administered Epi twice daily/13 weeks (long) or for two weeks (short). The long Epi administration induced a significant decrease in the amount of total and visceral fat and an increased lean mass. Besides, short Epi administration increased whole body BMD of the male offspring of the control and maternal obesity groups. In conclusion, the administration of long Epi protocol elicited better results in decreasing total fat and all fat deposits and increased lean mass. However, only the short Epi protocol increased the total BMD in the male offspring.