The team's first game was a 5–1 victory over Minnesota club
Inferno 95 in a friendly on May 15, 2005, at
Breese Stevens Field, with Jed Hohlbein scoring the team's first goal. The team finished 6–8 overall, third in the NPSL Midwest with a 5–5 record, behind NPSL champion
Detroit and
Milwaukee. Hohlbein was named to the inaugural NPSL All-Midwest team. In 2006, the Princeton 56ers were 12–2–4 overall and won the NPSL Midwest title with an 8–0–2 record. They lost to the
Sacramento Knights 2–0 in the NPSL championship game on July 29, 2006, with Anthony Chimienti and Alfredo Renteria scoring in the final 19 minutes. The game drew a team-record crowd of 1,351. Goalkeeper Eric Mickschl was named the NPSL Midwest MVP, while teammate Jed Hohlbein also made the All-Midwest team for the second time. In 2007, the team went 13–3–1 overall and repeated as NPSL Midwest champion with an 8–1–1 record. They lost to the
Southern California Fusion 1–0 in the NPSL semi-finals on July 27, 2007, in
La Mesa, California, then defeated the
Sonoma County Sol 1–0 in the third-place match on July 28, 2007. Midfielder
Brad Ring was named the NPSL Midwest MVP, and was joined on the All-Midwest team by goalkeeper Ryan Germann, defender Reed Cooper, defender-midfielder Tenzin Rampa and forward Jed Hohlbein. The 56ers made their debut in
U.S. Open Cup qualifying in 2007, as the NPSL representative. They lost to Detroit United 2–1 in the first round of the USASA Region II qualifying tournament on April 21. A match against German Fourth Division side
SC Wiedenbrück on June 23, 2007, was their first match against international competition. In 2008, the team went 7–3–2 overall and tied for second place in the NPSL Midwest with a 3–1–2 record. Henry Aiyenero was the team's leading scorer with five goals. Jed Hohlbein,
Brad Ring, Reed Cooper and midfielder Trevor Banks were named to the All-Midwest team. In the
2008 U.S. Open Cup, they won by forfeit over the Bloomington (Ind.) Cutters in the first round of Region II qualifying, then lost to
RWB Adria 2–0 in the semi-finals. In 2009, the team finished 8–3–2 overall and 5–2–1 in the NPSL Midwest, tying the
St. Paul Twin Stars and the
Chicago Fire NPSL atop the standings. The Twin Stars were awarded the regional title and a berth in the NPSL national semi-finals on a tiebreaker. Keith Dangarembwa led the team with four goals and was one of five 56ers players named to the All-Midwest team, joining goalkeeper Jon Szafranski, midfielder Pablo Delgado and defenders Trevor Banks and Brian Bultman. The 56ers made their debut in the
USASA Region II Amateur Cup, losing to
Croatia Cleveland 3–0, then defeating
FC Indiana 3–1 and Illinois'
AAC Eagles 5–3 at the competition in Oak Forest, Ill., but failing to advance to the final. In 2010, the team finished 10–7–2 overall and 8–2–0 in the NPSL Midwest, claiming its third regional championship. The 56ers lost to
Chattanooga FC 2–0 in the NPSL national semi-finals on July 29, 2010, and lost to
FC Sonic Lehigh Valley 3–1 in the third-place match on July 30, 2010. Brazilian Werebetth Rocha, known as Betinho, led the team with eight goals. Midfielder Trevor Banks was named to the All-Midwest team for the third time, while midfielder Keenan Newallo, defender Brian Bultman and goalkeeper Jon Szafranski were honored for the second time. Defender Sean Ronnekleiv-Kelly, in his first season with the team, also was an all-region selection. The 56ers finished 0–1–1 at the USASA Region II Amateur Cup, tying
Detroit United 1–1 and losing to Illinois' Inferno SC 3–0; their scheduled finale against
St. Louis Kutis SC was canceled due to field conditions with both teams out of contention for advancement. In 2011, the 56ers made their first appearance in the
U.S. Open Cup since starting the NPSL team. An earlier men's amateur team from the club qualified for the tournament in 1988, 1989, 1990 and 1991. In 2015, after winning the Midwest conference of the NPSL, the club switched to the second-year
Premier League of America. ==Alumni==