Planting multifunctional trees (e.g., fruit species) in cities can promote genetic conservation, economic activity, ecosystem services, and social cohesion. However, in Indonesia, the relationship between the abundance of fruit tree species and different city characteristics, including their involvement in the national smart city project, is still unknown. In this study, published reports and field surveys were used to evaluate the fruit tree distribution and its relationship with the characteristics of 224 of 514 Indonesian cities in order to identify tree species for multifunctional city greenery. This is the first study on the distribution of fruit tree species at the national level. The study identified 151 fruit species of 90 genera and 40 families, including large-sized fruits, such as avocados, breadfruit, coconuts, durians, jackfruit, and mangos. On average, cities contained 54 tree species, of which 21 (38.9%) were fruit trees. These findings indicate that cities are important contributors to the genetic conservation of local fruit trees, which can be further evaluated as new city greenery. However, a city’s involvement in the smart city project bore no relationship (p > 0.05) with the number of identified fruit species. Conversely, non-fruit species tended to be more diverse in smart cities. Since the presence of fruit species is associated with the city population, geographic position, climate, altitude, and attitude towards the fragility of sustainable conservation, introducing and maintaining these species as city greenery requires advocacy to city stakeholders.