Apuzzo was born in Cumberland, Maine and attended Colby College. He wrote for the Waterville Morning Sentinel while in college. He then worked for The Standard-Times in New Bedford, Massachusetts before moving to the Associated Press. He reported on New York City Police Department corruption and misconduct and revealed its collaboration with the CIA to conduct surveillance in Muslim communities. He won the 2012 Pulitzer Prize for Investigative Reporting with Adam Goldman, Eileen Sullivan and Chris Hawley.
In 2013, it was revealed that the Justice Department secretly subpoenaed his phone records as part of leak investigation into who provided the Associated Press information about a bomb plot foiled by the CIA. It was later revealed that the Justice Department had conducted leak investigations into his stories twice before. He has been highly critical of government secrecy and the media's willingness to accept it.
In 2015, a New York Times front page story by Matt Apuzzo and Michael S. Schmidt about the Hillary Clinton email controversy drew criticism for inaccuracies. Apuzzo and Schmidt had reported that inspectors general had filed a criminal referral to the Justice Department on Clinton over her handling of classified information. Kevin Drum wrote, "virtually everything about the story turned out to be wrong." Though the FBI did open an investigation, the referral was a "security referral."  It turned out there was a criminal investigation into the emails, according to The Washington Post. The newspaper reported that Justice Department granted immunity to the man who set up the server for Clinton. In fact, FBI Director James B. Comey would later say in a May 2016 interview with reporters that Clinton's description of the FBI probe had left him baffled: "I don't even know what that means. I'm not familiar with the term security inquiry." He added: “We’re conducting an investigation. That’s the bureau’s business. That’s what we do. . . . It’s in our name.”
In December 2015, another New York Times story by Apuzzo and Schmidt (written together with Julia Preston) criticized the US government for missing crucial evidence during the visa vetting process for a woman who would later become one of the shooters in the San Bernardino attack. The director of the FBI dismissed the reporting as "garble" and it turned out that rather than having "talked openly on social media about her views on violent jihad" as stated in the New York Times article, the woman had mentioned these in private communications.
The public editor of the New York Times called for "systemic changes" after these two erroneous articles by Apuzzo and his coauthors, which both relied on anonymous government sources. These problems were described as a "red alert" highlighting the need for more diligent and skeptical reporting and editing.
- Riedel, Bruce (September 10, 2013). ""Enemies Within: Inside the NYPD's Secret Spying Unit and bin-Laden's Final Plot Against America," by Matt Apuzzo and Adam Goldman". Lawfare Blog. Retrieved December 19, 2015.
- Byers, Dylan (December 19, 2013). "AP's Matt Apuzzo to New York Times". Politico.
- Calderone, Michael (May 13, 2013). "AP Phone Records Seized By Justice Department As War On Leaks Continues". Huffington Post.
- Calderone, Michael (September 3, 2013). "AP's Matt Apuzzo And Adam Goldman Crack Open Secretive Institutions, From NYPD To CIA". Huffington Post.
- Wheeler, Marcy (June 12, 2008). "Matt Apuzzo Pushes Back". emptywheel.net.
- Calderone, Michael (December 19, 2013). "AP's Matt Apuzzo Joins The New York Times". Huffington Post.
- Sullivan, Margaret (July 27, 2015). "A Clinton Story Fraught With Inaccuracies: How It Happened and What Next?". New York Times. Retrieved December 19, 2015.
- Drum, Kevin (December 16, 2015). "Strike Two for Pair of New York Times Reporters". Mother Jones. Retrieved December 19, 2015.
- Lipton, Eric (September 24, 2015). "Hillary Clinton Email Inquiry Weighs if Aides Erred at ‘Send’". New York Times.
- Hamburger, Tom (October 7, 2015). "FBI probe of Clinton e-mail expands to second data company". Washington Post.
- DeYoung, Karen (July 24, 2015). "Probe sought into possible ‘classified’ details in Clinton private e-mails". Washington Post.
- Sullivan, Margaret (December 18, 2015). "Systemic Change Needed After Faulty Times Article". New York Times. Retrieved December 19, 2015.