In 2008 Dutch media reported that Kruys would sign a 4+1⁄2-year contract with Malmö FF, and he eventually joined the team in July 2008.

[11] He then left the position in 2014 and started working as a youth coach and assistant manager at VV De Meern, still playing for SBV Excelsior beside.

[16] On 16 June 2022, VVV-Venlo appointed Kruys as head coach on a two-year deal, effective from 1 July 2022, replacing Jos Luhukay.

[17] In March 2024, he announced his decision not to renew his expiring contract at the end of the season, stating, "It was a very difficult choice, but I feel it's time for a new challenge.

"[18] On 4 June 2024, Kruys was announced as head coach of newly relegated Eerste Divisie club Volendam, a team he also represented during his playing career.