Koenders is a defender who was born in Amsterdam. He began his career at SDZ before joining the Ajax youth department in 1996. He left Ajax after 10 years, in 2006. Koenders then joined to RKC Waalwijk and made his debut in the professional football in the 2006–07 season, playing 30 matches. After 1 year, he left the club in 2007, and moved to AZ Alkmaar. In January 2009, he was loaned out to N.E.C..
He was once again loaned out in early 2010, this time to Sparta Rotterdam. In the summer of 2010, he signed another loan contract, now at NAC Breda.