The Boston Phoenix was one of the first newspapers to provide extensive coverage of the GLBTQA community's fight for civil rights. A May 29, 1987 issue of The Boston Phoenix included condoms, as well as an eight-page brochure insert that provided explanations of  safe sex practices during the AIDS crisis. The AIDS epidemic was frequently written about in The Boston Phoenix, shedding light on a topic other local papers avoided. In 1992, The Boston Phoenix became one of the only local newspapers to feature personal ads for individuals that were HIV-positive in their dating column “HIV-Positive.” In 1993, WFNX’s One in Ten program inspired a special section in the print edition of the newspaper, to expand The Boston Phoenix’s existing column on LGBTQ news.

In 2001, The Boston Phoenix broke the Boston-clergy sex abuse scandal in Kristen Lombardi’s ground-breaking cover story “Cardinal Sin.” Her article investigated the 25-plaintiff civil lawsuit against Father John Geoghan of the Boston Archdiocese and additionally named Boston’s archbishop Cardinal Bernard Law, as a defendant. Geoghan’s history of sexual abuse, his failed treatments, and his numerous reassignments by the Church in an attempt to hide the truth were uncovered. The Boston Phoenix and Lombardi continued coverage of Cardinal Law and the sex abuse scandal through 2003. The Boston Phoenix also made national headlines in 2002 when they linked to a video of the beheading of journalist Daniel Pearl on their website.

Many prominent journalists began their careers at The Phoenix. Some notable journalists include Joe Klein, a former news editor who became a political columnist for Time magazine; Sidney Blumenthal, a former reporter who became an aide to President Bill Clinton and a contributor to several national publications; Janet Maslin, a former rock music critic who became a film and literary critic for The New York Times; and David Denby, a former music and film critic who became a staff writer at The New Yorker. On the local level, Alan Lupo, Boston Globe columnist, and Chris Faraone, who covered Occupy Boston and authored 99 Nights with the 99 Percent, also worked at The Boston Phoenix.

 The Phoenix has received many awards for excellence in journalism, including honors from the New England Press Association (2007, 18 awards including first place for general excellence; 2016, Stephen Mindich inducted into the New England Newspaper Hall of Fame), the American Bar Association Gavel Awards (1984, “Life Before Death,” a four-article series on death row inmates), and the ASCAP-Deems Taylor Awards (2003, Jon Garelick, “Giving Jazz the Business: Can Major Labels Make the Music Pop?”; 2011, David Thorpe “What would Jesus Download? Who Charted? Billboard’s Top Christian Songs Edition,” and “Deluxe Buyer’s Guide: The Word on Seasonal Box Sets”). In 1994, Phoenix classical-music writer Lloyd Schwartz was awarded a Pulitzer Prize for criticism.

The Boston Phoenix went online in 1994 featuring 90% of the print edition. In addition to providing audiovisual content to supplement the print edition, the website also featured numerous blogs including, On the Download, covering music and entertainment; Talking Politics, featuring political writer David S. Bernstein; and Phlog, which covered general news. On September 20, 2012, The Boston Phoenix merged with Stuff to become a new glossy magazine titled The Phoenix. Its final print edition was distributed on March 15, 2013 and the final edition was published online a week later on March 22, 2013.