Being a trained lawyer, Heiko Warnken joined BMZ in 1991. Since the BMZ fosters a culture of constant professional rotation, he worked there in different country teams on Syria, Egypt, Bangladesh, Afghanistan) but was also happy to work for more than 10 years abroad (based as head of cooperation in the German Embassies in Ethiopia, Kenya and India).

From 2009 onwards, Warnken headed different sectoral departments including the Department for Environment and Sustainable Resource Protection (dealing among others with Biodiversity and Forest Conservation, the Forest Carbon Partnership Facility, Preparation for Rio +20 summit and later the Division for Sustainable Agriculture, Forestry, Soil, and Land Rights (comprising UNCCD, Forest Landscape Restoration, Central African Forest Initiative (CAFI), Congo Basin Forest Partnership, cooperation with Rights and Resources Initiative, establishment of the ProGreen Fund with the World Bank).