Abstract The paper reports on generalisations drawn from the author’s historical analysis of a sample of some five thousand words, which reflect more than two hundred lexical items from up to sixty-six Central Chadic languages and language varieties. The paper provides illustrative examples from present-day languages with explicit diachronic analyses of the evolution of their synchronic segmental and ‘prosodic’ suprasegmental structures. Four typologically characteristic prosodies (i.e., palatalisation, labialisation, nasalisation, glottalisation) operate across words, which are – in synchronic perspective – mostly monomorphemic, while in diachronic perspective they are mostly polymorphemic. The paper shows that, and how the four reconstructed prosodies lead to the diachronic emergence of innovative phonemes in the modern languages, which were not part of the segmental phonological inventories of the common proto-language. This empirical fact poses considerable challenges to the application of the well-established ‘comparative method’ as originally developed by the Neogrammarian school of historical linguistics.