Tanduay would disband before the 1988 season, but the franchise rights were bought by the Purefoods. Fernandez would become playing coach, his first coaching stint, of a young team composed of Jerry Codiñera, Jojo Lastimosa, Al Solís, Glenn Capacio and later Alvin Patrimonio. In the 1988 Open Conference, he led his new team to a runner-up finish to San Miguel Beer. However, midway through the All-Filipino Conference, he would relinquish his coaching duties to his assistant, Cris Calilan, to concentrate on his game. But in a controversial move, Fernandez was benched during the Finals against Añejo Rhum. The said event led to his transfer to San Miguel Beer in exchange for, the second time, Abet Guidaben. Fernandez would later lead the Beermen to the 1988 Reinforced Conference Championship and also won his fourth MVP Award, becoming the first and the only player to win four MVP awards with four teams.