The role of urban trees in the climate change discourse is not well articulated due to limited data. Understanding the factors that influence the role of urban forests and their species in carbon storage, an important issue in climate change will be essential in this respect. Arguing that multipurpose trees are likely to be preferred in urban forests in developing countries due to the varied and numerous benefits that planters derive from them. Carbon stock in urban forests of Niamey and Maradi in Niger, across land use/cover types, was estimated to ascertain the contribution of multipurpose trees. Niamey is the political capital of Niger, which is traversed by the Niger River. While Maradi is the economic capital of Niger and closest city to Kano, Nigeria. The two cities are sahelian with contrasting urbanization plan. Data were collected on neem trees and all other species with a diameter at breast height ≥ 5 cm using stratified random sampling. We quantified total biomass (above and belowground biomass) and carbon equivalent in seven urban land use/land cover types using non-destructive methods. Our findings showed that A. indica stored more carbon than any other species in the cities’ urban forests. It accounted for 54% and 61% of carbon stocks in urban forests of Niamey and Maradi respectively with a mean of 26.66 ± 7.64 t/ha in Niamey and 34.66 ± 10 t/ha in Maradi. In both cities, the proportion of the urban forests’ carbon stocks held in neem varied significantly across land use/land cover types (p < 0.05). In Niamey urban forests in commercial areas had the highest carbon stock (67.05 ± 27.49 t/ha) whilst in Maradi the highest carbon stock (78.02 ± 25.7 t/ha) was found in urban forests along roads. The neem tree’s carbon stocks in Niamey and Maradi should be taken into account during urban land use planning for carbon conservation and carbon stocks enhancement, which are key to atmospheric CO₂ reduction. The results suggest that carbon stocks enhancement in urban forests can be promoted through the use of multipurpose trees. The findings complement the international tree carbon dataset and reference level from Sahel city for climate change mitigation.