Zubiri announced his resignation from the Senate on August 3, 2011, following allegations of poll fraud during the Senate elections of 2007. He is the first Philippine Senator to do so, since all historical resignations from the Senate prior to his resignation involved senators leaving to assume other positions in government.
Zubiri was born in Makati City, Philippines to a Negrense father, Jose Maria Rubin Zubiri, Jr. from Kabankalan City and a Bicolana mother, Maria Victoria Ocampo Fernandez of Libon, Albay who was raised in the province of Bukidnon in Mindanao. He speaks Cebuano, Tagalog, English, and his father's native Hiligaynon. His father Jose Maria is the incumbent Bukidnon provincial governor.
Zubiri finished elementary and high school in Colegio San Agustin-Makati. He graduated from the University of the Philippines Los Baños with a degree in Bachelor of Science in Agribusiness Management. He also earned a Master of Environment and Natural Resources Management degree from the University of the Philippines Open University.
After serving as chief of staff of his father, Rep. (now Bukidnon Governor) Jose Ma. R. Zubiri, Jr., from 1995–1998, he ran for the seat representing the third district of Bukidnon to be vacated by his father in the 1998 general elections. Winning easily in that election, he served his first term in the 10th Congress. During his first term, he was one of the members of what the media dubbed as the "Spice Boys", a group of neophyte and two-term congressmen who were openly critical of President Joseph Estrada's administration. He was subsequently re-elected to the Philippine House of Representatives in the 2001 and 2004 elections.
After serving as a Congressman for three-terms, he was drafted by Lakas CMD to be one of their candidates in the pro-Macapagal-Arroyo administration Team Unity ticket in the 2007 mid-term elections.
In the final tally for the 2007 senatorial race by the Philippine Commission on Elections (Comelec), Rep. Zubiri narrowly defeated opposition candidate Aquilino Pimentel III for the 12th and last slot in the Senate. Zubiri had a total of 11,001,730 votes against Pimentel's 10,983,358 votes. The margin of some 18,372 votes was hotly contested, particularly the votes from the southern Philippine province of Maguindanao, where Pimentel had lost heavily to Zubiri.
Claiming the votes in Maguindanao were tainted, Pimentel petitioned the Philippine Supreme Court to invalidate the votes from Maguindanao, effectively disenfranchising a whole province. The Supreme Court voted unanimously 14 -0 against Pimentel and allowed the COMELEC (Commission on Elections) to count the votes in Zubiri's favor. Pimentel then returned to the Supreme Court for the second time. This time, he petitioned the justices to issue a restraining order against the proclamation of Zubiri. After oral arguments, however, the High Tribunal again voted to uphold the COMELEC's decision to proclaim Zubiri, consequently failing to grant Pimentel's petition. The next day, July 14, 2007, Zubiri was duly proclaimed elected to the Philippine Senate. However, the Court's judgment did not prevent Pimentel from bringing his poll protests to the Senate Electoral Tribunal.
On March 14, 2008, the Supreme Court, in a 40-page decision penned by Associate Justice Minita Chico-Nazario, dismissed Aquilino Pimentel III's petition to stop the Commission on Elections from canvassing votes from the province of Maguindanao, a definite morale booster for Senator Zubiri.
While serving his stint in the Senate, Zubiri began advocating a more in-depth study of biofuels in order to prevent food shortages, all the while allowing current production of alternative clean energy and biofuels so as to lessen dependence on imported oil and allow the Philippine economy a new avenue of economic success, "especially in this day and age of constant rising oil prices".
On August 3, 2011, however, during his privilege speech on the floor in the Philippine Senate, Zubiri suddenly announced his resignation from the body. In his speech, he said that his family was hurt by the "unfounded" accusations against him. "Without admitting any fault and with my vehement denial of the alleged electoral fraud hurled against me, I am submitting my resignation as a duly elected Senator of the Republic of the Philippines in the election for which I am falsely accused without mercy and compassion," Zubiri said in his speech. "My political detractors began calling me ugly names and dragging the name of my family in entirety. In other words, Mr. President, the trial by publicity has begun," he continued.
His resignation was lauded by Malacañang and various sectors but was also seen as a step that helped restore the Filipino's faith in national electoral protests.
Senator Francis Pangilinan, a member of the Senate Electoral Tribunal, likewise refused to comment on what the next procedure is for the vacancy left by Zubiri. "Let's just wait for developments if any," he said.
In 2016, he ran for the senate under the Partido ng Galing at Puso of Senator Grace Poe's presidential campaign placing 6th in the polls.