Canopy phenology is sensitive to variability in local environmental settings. In temperate climates, urban phenological processes and their determinants are relatively well understood. Equivalent understanding of processes in tropical urban settings is, however, less resolved. In this paper, we explore the influence of local urban environmental characteristics (that is, degree of urbanization, land cover and urban climate) on canopy phenology of two deciduous tree species (Jacaranda mimosifolia, n = 48, and Tabebuia rosea, n = 24) in a tropical city (Kampala, Uganda). Our study design involved ground monitoring and field sampling in 2017, with a focus on the dry season. We found that both species experienced significantly higher rates of canopy cover decline in heavily built-up neighborhoods (p < 0.05 for both species). Moreover, Jacaranda was more sensitive to differences in the degree of urbanization than Tabebuia, both in terms of total percentage tree canopy cover (p < 0.01) and net leaf loss (p < 0.05). Total percentage tree canopy cover for Jacaranda declined with increasing proportion of impervious cover (that is, roads and paved cover) and was positively related to relative humidity (p < 0.01), a variable correlated with soil moisture. Net leaf loss in Jacaranda increased with the decreasing proportion of pervious land cover and as nighttime air temperature increased (p < 0.01). In contrast, land cover and urban climate had no significant influence on either measure of phenological traits for Tabebuia. These results provide new evidence of the effect of urbanization on canopy phenology of different tree species in the tropics. Such knowledge offers new insights into the spatial and temporal differences in the physiological functional traits of trees and also serves as a proxy for possible species responses under future climate change.