In 1986, a small group of former members of Cypriot Community's Soccer Club, Central City, met at 15–17 Heffernan Lane.

After making a huge fund raising effort and gathering together 150 foundation members they were able to take over Greensborough SC and move it to Victory Park in the City of Moorabbin.

That year the club finished runners up to Chelsea on goal difference, achieving promotion to Victorian League Division 4.

[6] Bentleigh brought in a number of high-profile players for the 2015 season, including the likes of Daniel Visevic, Steven Topalovic and Queensland trio Troy Ruthven, Matt Thurtell and Chris Lucas.

The season hit a major snag when the Greens were knocked out of the 2015 FFA Cup in the qualifying stages by the unfancied Ballarat Red Devils but ended in fine style with the club winning its first-ever major title when it beat South Melbourne at Lakeside Stadium in the Grand Final, 3–1 after extra time.

[7] Bentleigh finished runners-up to South Melbourne in the regular season, missing out on the minor and major double on goal difference.

[14] Bentleigh were drawn against Adelaide-based side North Eastern MetroStars in the Round of 32 of the FFA Cup in 2016,[15] winning on penalties, with the game tied at 2–2 after 90 minutes and 3–3 after extra time.

[17] Battling torrential rain and a stubborn Strikers side, it took extra time for Bentleigh to win through to the quarter-finals, with Matthew Thurtell scoring the game's lone goal in front of 3,000 fans at Valley Road.

[21] In preparation for the 2017 season, Bentleigh lost Kamal Ibrahim to Avondale FC and Liam McCormick to South Melbourne.

[22][23] After a fourth-placed league finish, Bentleigh secured its second NPL Championship in three years when it beat Heidelberg United 2-1 after extra time in the Grand Final, with Ross Honos scoring in the 106th minute to win the tie.

[24] Bentleigh became the 6th member federation side in FFA Cup history to knock out an A-League opponent when it beat Wellington Phoenix FC 1–0 at Kingston Heath in August 2018.

[29] Anastasiadis' last game in charge was an NPL Victoria Round 13 victory over the previously undefeated Avondale, propelling the Greens to second spot on the table.

Tolios led the Greens to a 2–1 victory over premiers Heidelberg and a penalty shoot-out win over Avondale in the NPL Victoria Grand Final at AAMI Park to make it three championships in five years for the Cheltenham-based club.

[32] For 2023 Season, Bentleigh Greens made the direction to appoint Alfredo Costantino as the club's first-ever full-time senior coach.