Kipyego's only major competition appearance of 2006 came at the 2006 IAAF World Athletics Final and he narrowly finished out of the medals in fourth place. He gained selection for the long race at the 2007 IAAF World Cross Country Championships and won his second career team title through his sixth-place finish. He finished second to Richard Mateelong at both the national trials and the African Championships (his first podium finish in the event as a senior). He dipped under 8:10 minutes at the Weltklasse Zurich meeting later that year, recording 8:09.05 minutes (making him the fifth fastest man that year) and taking third behind Koech and Mahiedine Mekhissi-Benabbad. He ran at the 2008 IAAF World Athletics Final in Stuttgart, but managed only eighth place. In 2009 he did not gain an international spot for Kenya, but had some success on the European circuit, improving his personal best to 8:08.48 minutes in a runner-up performance at the Herculis meeting and taking seventh at the 2009 IAAF World Athletics Final.