Monitoring land surface phenology (LSP) trends is important in understanding how both climatic and non-climatic factors influence vegetation growth and dynamics. Controlling for land-cover changes in these analyses has been undertaken only rarely, especially in poorly studied regions like Africa. Using regression models and controlling for land-cover changes, this study estimated LSP trends for Africa from the enhanced vegetation index (EVI) derived from 500 m surface reflectance Moderate-Resolution Imaging Spectroradiometer (MOD09A1), for the period from 2001 to 2015. Overall end of season showed slightly more pixels with significant trends (12.9% of pixels) than start of season (11.56% of pixels) and length of season (LOS) (5.72% of pixels), leading generally to more ‘longer season’ LOS trends. Importantly, LSP trends that were not affected by land-cover changes were distinguished from those that were influenced by land-cover changes such as to map LSP changes that have occurred within stable land-cover classes and which might, therefore, be reasonably associated with climate changes through time. As expected, greater slope magnitudes were observed more frequently for pixels with land-cover changes compared to those without, indicating the importance of controlling for land cover. Consequently, we suggest that future analyses of LSP trends should control for land-cover changes such as to isolate LSP trends that are solely climate-driven and/or those influenced by other anthropogenic activities or a combination of both.