However the contract was terminated mutually with national team after a conflict with the FC Flora chairman Aivar Pohlak, who was the head of the Estonian Football Association at that time.

Pijpers however disagreed and after a poor start to the 2010 FIFA World Cup qualification campaign, he was fired by the Kazakhstan Football Association as they felt he was not being aggressive enough.

In July 2007, whilst continuing as Kazakhstan's Manager, Pijpers took up the role as Consultant at FC Alma-Ata in preparation for their UEFA Cup debut.

[5] The Dutchman returned to Estonia in late 2011 and became the technical director to help coordinate, analyze and guide the training operations across different senior and youth national teams.

[6][7] On 8 March 2012, he was appointed as the head coach of Estonia's under-19 national team for the 2012 UEFA European Under-19 Football Championship.