The Nuts adopted their current name in 2005 after the team's affiliation with the Oakland Athletics ended. Before then, the team was known as the Modesto Athletics (or A's) from 1975 to 2004. The club was also known as the Modesto Reds (1966–1974 and 1946–1961) and Modesto Colts (1962–1964).
The Nuts were expected to leave Modesto following the 2024 season after the city and the Seattle Mariners were unable to come to terms on who would pay for ballpark improvements mandated by Major League Baseball. However, a deal was reached to keep the team in Modesto through at least the 2025 season; following the end of the 2024 season, the Mariners sold the team to Diamond Baseball Holdings, who immediately announced that the 2025 season would be the last for the Modesto Nuts, and for the 2026 season, as part of a shuffle of Diamond-owned team relocations, the Nuts franchise would relocate to San Bernardino as a new incarnation of the Inland Empire 66ers.
In spring 2008, the team was the subject of Bush League TV's short internet video "Bush League 101: How to Bush League a Bush League Baseball Team."
On June 21, 2011, the Modesto Nuts hosted the 2011 California/Carolina All Star Smash.[2]
In 2012, Greg Young was replaced by Alex Margulies who did play-by-play for all home and away games from 2012–2013, and Modesto Bee sports writer Brian VanderBeek did color commentary in the middle innings of most home games. Keaton Gillogly did play-by-play from 2014-2022. The play-by-play position was formerly held by Joshua Suchon, who now works for the Los Angeles Dodgers.
On September 1, 2012, Modesto Nuts 1st basemen Jared Clark hit his 24th home run of the season against the San Jose Giants, making him the Modesto Nuts single-season home run leader, passing former Nuts outfielder Kent Matthes, who in 2011 set the old record with 23 home runs in the season.
As of 2011, the Modesto Nuts have set their attendance record for five straight seasons and have been honored as back-to-back California League Organization of the Year for 2010 and 2011.
Following the 2016 season, the Seattle Mariners purchased a majority share of the Nuts, and the teams entered into a player development contract making Modesto a Mariners affiliate. HWS Baseball IV, LLC, continues to see to the team's day-to-day operations.[3]
The Nuts won the California League championship for 2017, sweeping both the Division Series and the League Series and winning nine games in a row dating back to the last three games of the regular season.[4] This was the Nuts' ninth league title and the first as part of the Mariners organization.
In conjunction with Major League Baseball's restructuring of Minor League Baseball in 2021, the Nuts were organized into the Low-A West where they continued as a Mariners affiliate at the Low-A classification.[5] In 2022, the Low-A West became known as the California League, the name historically used by the regional circuit prior to the 2021 reorganization, and was reclassified as a Single-A circuit.[6] In 2023, Modesto won the California League championship.[7]
After the city and the Seattle Mariners were unable to come to terms on who would pay for the roughly $32 million in improvements to John Thurman Field mandated by Major League Baseball, the Nuts planned to leave Modesto after the 2024 season.[8] However, the city and the Nuts came to an agreement in August 2024 to keep the team in Modesto for another year. The Nuts will pay an annual rent of $600,000, and an additional $75,000 will go towards improving the field. A long-term lease agreement must be reached by April 1, 2025, or the team could leave following the season.[9]
A month after it was announced the Nuts would stay in Modesto for another year, they won their second straight California League title.[10]
The team was sold to Diamond Baseball Holdings on December 12, 2024.[11] Diamond, the largest owner of MiLB teams, plans a "musical chairs" format in the aftermath of the purchase:
The Nuts will move to San Bernardino and assume the Inland Empire 66ers nickname, but keep the Mariners' affiliation, reuniting the two for the first time since 2006.