He was successively appointed as reserve team coach of Fenerbahçe for the 2005–06 season, and then as Gertjan Verbeek's assistant at his former club SC Heerenveen from 2006 to 2008.

Under his tenure, the small Eerste Divisie side, mostly composed by youngsters on loan from the parent club (and thus all former players of Pastoor under his tenure at Feyenoord), went on to end the regular season in third place and qualify to the promotion playoffs, where they defeated crosstown rivals Sparta Rotterdam in a tense two-legged final and ensured a historic promotion to the Eredivisie.

[5] He was temporarily succeeded by Ron de Groot and Wilfried Brookhuis, Pastoor's former assistant and goalkeeper coach.

On 15 September 2014, Alex Pastoor was assigned as caretaker after health problems resulted in Marco van Basten having to step down to the position of assistant.

[9] During the winter break of the 2014–15 season, Pastoor was appointed the new head coach of second-tier Eerste Divisie club Sparta Rotterdam.

[12] In March 2019, Pastoor became coach of Austrian Football Bundesliga club SCR Altach, for whom he had already played as a player.

Under the Dutchman, the Vorarlberg side stabilised again and finally managed to stay in the league at the end of the season, eight points ahead of relegated Wacker Innsbruck.