[citation needed] Starting with the 2016 season, AFC Ann Arbor played in the National Premier Soccer League as part of the Midwest Region[3] under manager Eric Rudland, formerly of Lansing United.

[4] They finished in second place in the Great Lakes West Division in their first NPSL season, advancing to the national playoffs, but ultimately losing to AFC Cleveland on penalty kicks.

[citation needed] The 2017 season brought more success for AFC Ann Arbor as they won their first ever Great Lakes Division Championship and the inaugural Michigan Milk Cup in the process.

[5] They again advanced to the NPSL national playoffs defeating the Dayton Dynamo in the second record (having received a bye in the first round) before falling to Detroit City FC 3–2 in extra time in the Midwest regional final.

[16] The men's team finished third (7–3–4) in the USL2 Great Lakes Division behind Kalamazoo FC and Flint City Bucks,[17] missing the playoffs for the first time in five (non-suspended) seasons.

In the 2023 season, the AFCAA men's team found its way back to the postseason with a 2nd-place finish in the USL2 Great Lakes Division behind Flint City Bucks,[18] where they met first round opponents Thunder Bay Chill.

In 2022, because AAPS was not yet allowing rental of its facilities due to the pandemic,[21] the team played at Saline Hornet Stadium.