Following the 2016 season, a drastic shift in the Pecos League landscape occurred as two Kansas teams, the Salina Stockade and Great Bend Boom, both folded, while a third, the Topeka Train Robbers, moved to Bakersfield, California, taking the place of the former Bakersfield Blaze, who folded following the 2016 California League season.

They joined the all-California Pacific Division, and replaced the California City Whiptails and High Desert Yardbirds in the circuit.

The Pacific Division originally planned on enacting a similar format, but due to the ongoing pandemic, were unable to compete in 2020.

For the 2021 season, the Salina Stockade returned and the league announced the addition of the Colorado Springs Snow Sox as an expansion team.

On April 4, the league announced its final division alignment for the season, which did not include California City and High Desert after previously indicating each would return.

In April 2021, Yermín Mercedes was called up to the Chicago White Sox where he set a major league record as the first baseball player in modern MLB history to begin a season with eight consecutive hits.

For the 2022 season, the league announced three expansion franchises: the Santa Rosa Scuba Divers, Austin Weirdos, and Weimar Hormigas.

Before 2023, the league introduced 4 new teams; the Lancaster Sound Breakers, Marysville Drakes, Blackwell Fly Catchers, and Dublin Leprechauns.

The Weimar Hormigas, Colorado Springs Snow Sox, Wasco Reserve, and Santa Rosa Scuba Divers folded.