He first taught and researched at Ahmadu Bello University, Zaria, between 1962 and 1979, during which time he trained many students, built a map library, and edited the journal Savanna.
He was a consultant for DFID, CIFOR, the UNCCD, DANIDA, the Natural Environment Research Council, and the Drylands Development Centre in Kano.
Mortimore is known for his extensive studies of farming systems, environmental change and human adaptation to drought in the drylands of northern Nigeria, and comparative work in Kenya, Niger, and Senegal.
Wood fuel in Kano (with Reg Cline-Cole et al.) was an exhaustive study of the fuelwood market also conducted in the late 1980s following the major droughts.
Leaning on (and improving on) Ester Boserup's work, they discovered population growth and environmental enhancement occurred thorough multicropping and other farming methods, terracing, and strong community organisations.
Mortimore's comparisons of photographs from 1930 and 1990 revealed an improvement in landscapes and in resource management (rather than degradation and impoverishment, widely assumed to have been present), albeit with much higher population densities and altered labour regimes.
The 1993 launch of More People, Less Erosion at the ODI in London was electric – several staff members of the UK Department for International Development, the World Bank, and academic researchers from East Africa were there, and the study has echoed through revisionist thinking about African degradation myths and agrarian policy ever since.
He was a long-term critic of the argument that the Sahara is 'spreading' as a result of poor land management, or that farmers and herders tend towards destroying their natural capital.