Bernardino presided the league during the title reigns of the Sunkist Orange Juicers, Alaska Milkmen and resurgence of the Ginebra San Miguel franchise from 1994 to 1998.

However, with the rise of the newly formed Metropolitan Basketball Association in 1998, a regional-based professional league, Bernardino implemented a direct Filipino-American (Fil-Am) rule for each team for the 1999 season.

The first one surrounded on-court controversy, as Tanduay fielded an already questioned fil-am Earl Sonny Alvarado in Games Two and Three of the All-Filipino Cup semifinal series against the Purefoods Tender Juicy Hotdogs, despite the league's warning.

In 2001, Bernardino went through minor health problems and was forced to temporarily hand the reins to deputy commissioner Sonny Barrios to recuperate.

In 2004, Bernardino, along with Ricky Palou and other former PBA executives, formed Sports Vision Management and was responsible for the formation of the school-themed Shakey's V-League that began in 2004.

Jun Bernardino died at 1:30 a.m. on March 24, 2007 at the Makati Medical Center, from a heart attack after organizing a surprise birthday celebration for Philippine basketball pioneer Moying Martelino.