Villanueva first played for the Ateneo Blue Eaglets in the UAAP Juniors division leading them to numerous winning seasons and championships.

In his rookie season, he averaged modest numbers of 7.4 points and 4.5 rebounds playing a limited role as a reliever of veterans Davonn Harp and Mick Pennisi.

By season's end, he was included in the PBA Mythical Team but lost in the MVP race to Purefoods' James Yap.

In a four-team trade, Purefoods acquired Villanueva, sending energetic forward Marc Pingris to San Miguel (known as Magnolia at that time).

[4] While playing for Ginebra, he reunited with college teammates Rich Alvarez and Paolo Bugia, and was tasked to back up oft-injured Eric Menk.

On March 18, 2014, PBA Commissioner Chito Salud approved the trade that sent Villanueva to Air21 Express for Carlo Sharma and Ronnie Matias.

He also mentioned that the influx of younger, athletic, and bigger players has challenged him to “reinvent” himself to find his place in the rotation of incoming NLEX coach Boyet Fernandez.

He is remembered during the Champions Cup for pulling the leg of Sagesse Lebanon's Stephen Howard after an altercation, resulting in his ejection.

[12] Villanueva is vividly remembered for his on and off the court feud with former college rival and one-time teammate at Air21, Joseph Yeo.

Another incident happened during a 2006 PBA preseason game at the Emilio Aguinaldo College Sports Center in Manila when both players were reportedly involved in a physical and verbal exchange.