In 2007, Dan Frosch, now with The New York Times, won the Association of Alternative Newsweeklies' first-place prize (for under 60,000 circulation) for Investigative Reporting for his 15-part series, "The Wexford Files".

[10][clarification needed] In 2013, the Santa Fe Reporter filed a lawsuit against New Mexico Governor Susana Martinez,[11][12] alleging violations of the state's Inspection of Public Records Act[13] as well as a violation of the Free Press clause of the New Mexico Constitution.

[14][15] Attorneys for the newspaper and the government argued in court in March 2017,[16][17] and Judge Sara Singleton ruled in the case from her retirement in December of that year that the governor had broken the records law, but her actions did not violate the Constitution.

Its 2019 cohort was honored in 2020 by the Association of Alternative Newsmedia for the collaboration that covered sustainability programs at the Santa Fe Community College: “Roadmap to Resilience”[20] by Olivia Abeyta, Max Looft, Anna Girdner, and James Taylor under the direction of mentor and educator Julia Goldberg.

The Society of Professional Journalists Colorado chapter's "Top of the Rocky's" contest listed nine Santa Fe Reporter stories among its best in the region in 2017.