The growing access to Earth Observations and processing capabilities have stimulated the production of global and regional products that are commonly used to assess tree-covered habitats and their changes. The popularity of these products has led to their use for defining baselines and to assess progress in conserving natural habitats, in particular in the context of the conservation targets to 2020 set by the UN Convention on Biological Diversity. In this paper we reviewed three tree cover products commonly used over Sub-Saharan Africa: (i) MODIS Vegetation Continuous Field percent tree cover map, (ii) Global Forest Change map and (iii) TREES product. Over a systematic sample of 2045 map subsets, each having a size of 10x10 km², we calculated the extent of tree cover and tree-cover change from each product. Our statistical and spatial comparison shows significant discrepancies between the three products, which lead to uncertainties when assessing tree cover across varying ecosystems. These differences are highest in habitats where tree cover is fragmented or reaches medium density levels (open forests) and overlap with areas of high economic development potential, where habitat changes are likely to occur in the close future. We discuss these findings in the context of using these remotely sensed tree cover products to support current global biodiversity conservation policies.