The club was founded on 15 August 1931 as Stormvogels but soon renamed Windvogels. In 1947 they merged with a local gymnastics team to become Sportverening Spakenburg. They joined the Eerste Klasse in the 1970–71 season under coach Joop van Basten, father of legendary Dutch striker Marco van Basten, and clinched their first league title in 1974. They became champions again in 1985, when they also won the overall Dutch amateur league title, and in 1987, 2000 and 2008.
They joined the Topklasse for its inaugural season in 2010. In its first season, Spakenburg was one of only three clubs (the other ones being Rijnsburgse Boys and FC Oss) to declare themselves eligible for promotion to Eerste Divisie; despite that, Spakenburg failed to qualify to the competition finals as they ended the regular season in second place behind city rivals IJsselmeervogels.