Emmanuel has worked to control the bushmeat trade and protect endangered wildlife in Central and Eastern Africa. His main focus has been on supporting the work of African wildlife rangers in conflict affected areas by driving economic development in partnership with local communities. His work was primarily in the parks of eastern DRC, working to sustain the national parks through the country's 20-year civil war. Merode is the author of fourteen scientific papers and co-editor of the book Virunga: The Survival of Africa's First National Park.

On 1 August 2008, he was appointed Director of Virunga National Park by the Congolese government. He now lives at the park headquarters in Rumangabo, bordering the park's mountain gorilla sector. The park's 680 rangers are under his direction and much of his work is focused on protecting the park's wildlife, including critically important populations of mountain gorillas, elephants, okapis and chimpanzees. His first breakthrough was to broker an agreement between the Congolese government and rebel leader Laurent Nkunda to spare the mountain gorilla sector of the park from the ongoing civil war and to enable government rangers to redeploy in rebel territory. Negotiating the neutral status of environmental and sustainable development imperatives among the warring factions in eastern Congo became a recurring theme in Merode's approach to establishing Virunga National Park as a stabilizing presence in the war-affected Great Lakes Region of Africa.

Given the chronic insecurity and the succession of violent wars in eastern Congo, Merode and a team of over 3000 conservationists and development practitioners have focused their efforts on economic development initiatives in a large-scale attempt to bring greater stability to the region. In 2013 he assisted in the launching of the Virunga Alliance in an effort to drive the post-war economy of eastern Congo as an instrument for peace-building in the region. The initiative is based on 127 local institutions from the private sector, civil society and government agencies committing to the sustainable development of the parks resources, through tourism, rural electrification through clean energy, sustainable fisheries and agriculture. A major program aims to generate 80-100,000 jobs in the post-war communities around the national park, providing young Congolese men and women viable alternatives to engaging in conflict related activities.

At his swearing in ceremony, Merode remarked, "The intensity of the conflict in and around the park makes this a daunting challenge, but it is a great privilege to be working alongside such a dedicated and courageous team of rangers. I have real confidence in our ability to secure a future for the park to ensure that it makes a positive contribution to the lives of the people of North Kivu." His role in maintaining the Park's administration during the M23 Rebellion was covered in the Oscar-nominated British documentary Virunga.

He has spoken about his work and the work of the rangers of Virunga in a TEDxWWF talk, "A story of conflict, renewal and hope". Under his leadership, the Virunga park opened to the public again in 2014.