During his first term, Andaya was a member of the "Spice Boys", a group of young congressmen who were openly critical of President Joseph Estrada and his administration.

[5] His term in the 13th Congress was cut short in February 2006 due to his appointment as Secretary of Budget and Management by President Gloria Macapagal Arroyo.

He ran again successfully in the succeeding House elections of 2013 and 2016, serving uninterrupted as a congressman until 2019, after which his wife took over until her untimely death in July 2020.

[20] In September 2015, he defected to the Nationalist People's Coalition (NPC) and supported the 2016 presidential campaign of Senator Grace Poe (an independent).

[17] In May 2014, a banner story published by the Philippine Daily Inquirer implicated Andaya, among other officials of the Arroyo administration, in the Priority Development Assistance Fund scam.

It alleged that during his time as budget secretary, he received at least ₱255 million as "commission" for various projects implemented by the Department of Agrarian Reform.

[23] He later denied any involvement in saying that he had "not received any amount, whether in cash or in check, as commission from [Janet Lim-]Napoles, or from any of her staff or agents".

[24] In October 2013, plunder charges were filed at the Office of the Ombudsman by the National Bureau of Investigation against former-President Arroyo and other officials of her administration including Andaya in connection with the alleged misuse of the Malampaya gas fund.

[25] In December 2017, the Ombudsman charged Andaya, along with convicted plunderer Janet Lim-Napoles and former Agrarian Reform Secretary Nasser Pangandaman, with 97 counts of graft and malversation before the Sandiganbayan for their alleged involvement in the Malampaya fund scam.

Andaya's alleged role in the scam was his signing of the Special Allotment Release Order (SARO) which was "fraught with irregularities constituting badges of fraud".

[28][29] In October 2018, an administrative complaint was filed by the Presidential Anti-Corruption Commission at the Office of the Ombudsman against Andaya and his wife for his alleged misdeclaration of properties in his 2016 and 2017 Statements of Assets, Liabilities and Net Worth (SALN).

[35] On June 1, 2021, Andaya was driving his Toyota Land Cruiser in Barangay Palestina, Pili when two men aboard a motorcycle fired at his vehicle before fleeing.