Increasing and challenging environmental pressures are threatening coffee cultivation worldwide. One of the key strategies to mitigate the impact of such pressures is to incorporate crop wild relatives in the value chain. However, this is often restrained by the lack of knowledge concerning basic features, such as the number and type of wild populations, or current threats. To fill this gap in coffee cultivation, we studied the population structure and threats of Coffea racemosa Lour., a wild relative of the two principal traded species, Coffea arabica L. and C. canephora Pierre ex A.Froehner. Coffea racemosa is native from Mozambique, and is resilient to drought and most coffee pests. It also has a low caffeine level, with a high market potential as an alternative to coffee consumers who are caffeine-sensitive. ​ Therefore, it is considered a good candidate to be used in future breeding programs. However, the current distribution of this species in Mozambique and the factors that might threaten its sustainable use are unknown. In this study, we searched for the occurrence of C. racemosa to understand how the species is distributed in Mozambique and how populations are demographically structured. Considering the scenario of high forest fragmentation in Mozambique, we specifically addressed if (1) populations vary between fragmented patches and conserved forests; (2) natural regeneration is occurring; and (3) habitat fragmentation is affecting the population's demographic structure. Our results show a demographic populational structure that is stratified into large, medium, and small trees and seedlings, with the latter mostly being found in conserved forests. In contrast, no seedlings or small or large trees were found in the small city patches, which were only composed of medium trees. Overall, there was no evidence of regeneration in small patches. These first insights are essential for the conservation and management of C. racemosa in Mozambique.