He was technical coach of Eerste Divisie side Emmen.[1] He was also the coach of Telstar for two seasons and took the reins at Cambuur in February 2016.[2] In June 2016, he left Cambuur and became coach of Jong Ajax.[3]
On 17 June 2017, Keizer became the new coach of Ajax on a two-year contract, after managing the youth side in the previous season, thus replacing the Borussia Dortmund-bound Peter Bosz.[4] After 17 games, Ajax were second in the Eredivisie, ranking with five points behind the leaders PSV, and Keizer was fired on 21 December 2017, after losing a cup match on penalties against Twente.[5]
He received his first foreign job on 2 June 2018, replacing retired compatriot Henk ten Cate at Al Jazira Club of the UAE Pro-League.[6] On 8 November the same year, he was allowed to resign to take the job at Sporting CP, with his club unbeaten and in second place at the time.[7]
Keizer signed for the Lisbon-based club on a contract until 2021.[8] On his debut on 24 November, they won 4–1 against Lusitano in the fourth round of the Taça de Portugal, and in his first Primeira Liga match on 3 December, the club won 3–1 against Rio Ave.[9][10] Sporting completed a cup double in Keizer's first season, seizing both the Taça da Liga and Taça de Portugal in penalty shootout wins against Porto.[11][12] He was the first foreign manager to win the latter tournament since fellow Dutchman Co Adriaanse of Porto in 2006.[13] He left Sporting on 3 September 2019.[14]
On 13 October 2019, Keizer returned to Al Jazira on a two-year contract, after compatriot Jurgen Streppel left the Abu Dhabi-based club.[15] On 11 May 2021, he led the club to their third league title after beating Khor Fakkan 3–1; it was his first league title in his career.[16] Keizer would enter 2022 with a successful 5–3 victory on penalty shootout against Shabab Al Ahli and clinching Al Jazira their first super cup title.[17]
On 27 July 2023, Keizer was appointed as manager of Saudi Pro League side Al Shabab.[18] On 6 September 2023, it was announced that Keizer and Al-Shabab agreed to end his contract mutually.[19]