A sufficient intake of fruits can alleviate micronutrient deficiencies and reduces the risks of a number of associated diseases. In many parts of sub-Saharan Africa, however, the production and consumption of fruits are inadequate on average and in particular so in specific seasons. To better incorporate fruits into local food systems while addressing the challenge of seasonal availability, World Agroforestry (ICRAF) has developed a methodology based on “fruit tree portfolios” that selects socio-ecologically suitable and nutritionally important fruit tree species for farm production, to meet local consumption needs. We here present this approach and illustrate it with data from a case study involving Western and Eastern Kenya. The approach uses mixed methods to capture on-farm fruit tree diversity and seasonality at a household level (n = 600 in our case study), the months of household’s food security and insecurity (n = 600) and food consumption patterns at an individual level, to identify dietary gaps (n = 294 women and child pairs in our example). In our case study, 31 fruit tree species were reported on farms in our Western Kenya sample (9 of which were indigenous) and 51 (27 indigenous) in Eastern Kenya. In addition, the median number of food-insecure months per household was four (ranging from 0 to 9 months) in Eastern Kenya and three (0 to 12 months) in Western Kenya. Finally, using 24-h recalls the proportion of women that had consumed a fruit the day before the interview was around 55% in Western Kenya and 80% in Eastern Kenya, with consumption averaging 93 and 131 g, respectively. Using these parameters for each site and fruit tree phenology and food composition data sets, we derived context-specific recommendations that involve promoting 11 fruit tree species to address micronutrient gaps.