Background: With a rapidly growing young population, the African continent provides a high but barely exploited economic potential. Creating an African free trade zone is one of the African Union’s major initiatives to increase prosperity. Even though the AfCFTA has already come into force, its potential has not yet been fully exploited. This study investigates the logistics challenges associated with the AfCFTA and potential solutions and development paths for future value chains. Methods: The study builds upon a two-stage research process. First, applying the Nominal Group Technique with a group of 19 industry experts, current challenges and strategies to deal with them are conducted, and statements about potential development paths emerging from the AfCFTA are synthesized. Second, a questionnaire among additional industry experts is done to assess the results of the first stage. Results: The article sheds light on the barely untapped field of logistics challenges hindering the AfCFTA to leverage its potential. Strategy fields to address current challenges are explained, and the first indications of how the AfCFTA will shape supply chains in the mid-term are outlined. Conclusions: The article underlines the importance of logistics in the development of pan-African value chains and highlights potential development paths that may arise in the medium term. It also emphasizes the growing need for cooperation between politics, business, and research to overcome current logistics challenges and leverage the potential of the AfCFTA.