Alaska drafted former FEU bruiser and current Gilas Pilipinas pool member Carl Bryan Cruz during the 2016 PBA Special Draft. They started the 2016–17 PBA Philippine Cup with key players Sonny Thoss, Calvin Abueva and Noy Baclao in the injured list forcing Cruz, sophomore stretch player Jaypee Mendoza and Marion Magat playing at the center slot. Due to lack of size, the Aces lost their first two games and initiated a deal to send swing man Rome Dela Rosa to Star Hotshots in exchange for former San Beda teammate big man Jake Pascual. Pascual immediately contributed to the team with his scrappy plays and defense and with Abueva and Manuel returning to top form, Alaska won its next three games. Despite finishing second in the standings and gaining a twice-to-beat advantage, the Aces, hampered by injuries, failed to enter the semi-finals when they lost two in a row to Barangay Ginebra. A week after their Philippine Cup campaign, Alaska traded back up point guard RJ Jazul to the Phoenix Fuel Masters in exchange for guard Simon Enciso.