Having a historical-comparative approach this paper is concerned with the reconstruction of some Proto-Nubian derivational morphemes comprising two causatives, two applicatives, and two suffixes deriving verbal plural stems, as well as a now defunct causative prefix. When discussing applicatives in the Nile Nubian languages, it is argued that they involve converbs, i.e., dependent verbs, which in Old Nubian and Nobiin are marked by the suffix -a. This verbal suffix is considered to be distinct from the homophonous predicate marker -a which occurs as a clitic on various other hosts. The paper also points out that some of the Nubian verb extensions correspond to Nyima (mostly Ama) extensions, thus providing strong evidence of the genetic relationship between Nubian and Nyima. Perhaps the most striking evidence of Nubian–Ama relations and the coherence of the Nilo-Saharan phylum as a whole is provided by the archaic Nilo-Saharan *ɪ-. The reflexes of this prefix in Nubian and Ama, along with the archaic Nubian prefix *m-, which serves as verbal negation marker, supports Dimmendaal’s hypothesis that these languages have undergone a restructuring process from originally prexing to predominantly suxing languages.