Ecological footprint (EF) and human development index (HDI) are two critical indicators for assessing sustainable development worldwide. Past studies in Africa have ignored dynamic sustainable total-factor ecological efficiency (DSTFEE) assessment. This present study proffers a novel dynamic sustainable total-factor ecological efficiency (DSTFEE) that comprehensively assesses the ecological efficiency among 44 sampled African economies from 2010 to 2016. Our study incorporates EF and HDI in the model. Second, the study evaluates regional DSTFEE heterogeneity efficiency as well as the technological gap efficiency in Africa. Further, projection analysis is done to offer a viable solution path to address the inefficient African countries. Third, the study investigates the determinants of ecological efficiency using the bootstrap truncation regression technique. The results from the implemented models are as follows: first, the DSTFEE for the 44 sampled African countries is very low (0.403), indicating enormous potential for improvement. Second, the heterogeneity of DSTFEE across the five Africa regional blocs is evident. The southern bloc had the highest efficiency score, followed by the northern, central, western, and eastern regions. The technology gap ratio also reveals a massive gap among the five Africa regional blocs. Third, the bootstrap truncation regression results established a U-shape nexus between growth and DSTFEE in Africa. REC and trade openness is positively corrected to DSTFEE for African countries. In contrast, financial development, foreign direct investment (FDI), and urbanization impede dynamic ecological efficiency in Africa. The study’s results equip African countries with adequate knowledge of their ecological efficiency situation and provide them a viable path to improve environmental efficiency, thereby boosting their ecological sustainability.