The club came into its current formation in 1995 after the fusion of two clubs from Watergraafsmeer, Jeugd Organisatie Sportclub and Watergraafsmeer. The Watergraafsmeer club was a result of six clubs amalgamating into one, TIW, Amstel, RNC, TDO, WMHO and Ontwaakt. Former manager and head coach of local giants AFC Ajax, Rinus Michels began his coaching career at JOS, managing the club from 1960 until 1964 before moving to AFC for a season, and then to Ajax a year later. Former Ajax player and Dutch Olympian Jaap Knol was the chairman of the club at the time. Former players who later made the step over to a professional club include Ruud Suurendonk, Johnny Beun, Jos Dijkstra and Ab Parree. JOS has been known to be a feeder club of sorts for AFC Ajax. The singer Henk Hofstede of the Dutch pop groupThe Nits wrote the song "JOS days" on the albumIn the Dutch mountains about the club. In the song he sings about the monument of War victims and speaks on the shameful fact of not being accepted at the club as the first born of the family. The monument of JOS has since been demolished, there are however still monuments dedicated to fallen members of football clubs from the War that are still standing elsewhere in the Netherlands.
JOS Watergraafsmeer's Sunday first team were promoted to the Hoofdklasse ahead of the 2009-10 season, where the finished in 3rd place. The top 3 clubs are automatically promoted leading to JOS competing in the Sunday Hoofdklasse A the following season, relegating back to the Eerste Divisie. In 2014, the club's Sunday team were promoted back to the Hoofdklasse, playing on the highest level of Amateur football and the fourth tier in the Netherlands once more. While competing in the 2014–15 KNVB Cup, the team advanced to the Second Round of the competition after defeating VV Noordwijk in a 2–1 win, where they then faced the first team of AFC Ajax marking the first official Amsterdam derby to be contest in the city since 1983. On 24 September 2014 the two teams meet at the historic Olympic Stadium where JOS Watergaafsmeer would be eliminated in a 9–0 loss, in which Ajax striker Arkadiusz Milik scored six goals. Davey van ’t Schip, the Son of former Ajax player and assistant managerJohn van 't Schip was playing for JOS Watergraafsmeer in the match as well.
