In 1997, Pérez left Lazard to set up Next Century Partners, a private equity firm based in Singapore, teaming up with Patrick Go, Dennis Mendiola, John Wallace, and Eduardo Martinez-Miranda.

[7] In early 2001, Pérez was recruited by his former academic adviser and then-newly sworn Philippine president Gloria Macapagal Arroyo to join her administration.

He dealt with solving the frequent grid-wide power black-outs that were hampering the economy then,[9] and had to secure the oil supply of the country in the wake of the 2003 Iraq War[10] by pursuing energy diplomacy in Asia and the Middle East.

[15] Since his return to the private sector in 2005, Pérez has been active in renewable power, energy advisory, and conservation issues.

He was a 2005 World Fellow[16] at Yale University, where he lectured an MBA class on renewable power in emerging countries.

That same year, he was invited by the owners of NorthWind, the first wind farm in Southeast Asia, to replace a minority shareholder, and that led him to a decade-long career investing in renewable energy.

[18] On March 19, 2024, the Department of Energy awarded Perez’s Alternergy Holding Corp. a “Certificate of Confirmation of Commerciality” which essentially is a green light for its Alabat and Tanay wind projects.

[22] He is a member of the advisory boards of Bhutan Foundation,[3] New Zealand Trade and Enterprise,[23] Geneva-based Pictet Clean Energy Fund, and the Yale Center for Business and the Environment.

In 2000, he co-founded Asian Conservation Company, an innovative venture philanthropy with like-minded conservationists, and together they acquired El Nido Resorts.

With a management team from Next Century Partners, they transformed it into an award-winning eco-tourism destination in Palawan[24] and then sold it to Ayala Land in 2013.

Pérez has long been involved with World Wide Fund for Nature (WWF) starting with arranging debt-for-nature swaps.

Together with his sailing buddy Judes Echauz, they won the Rolex China Sea Race on their yacht Subic Centennial, first in 1998 and again in 2008.