This paper provides proposals for the internal reconstruction of Bena-Yungur [Glottocode: bena1260]. The present-day three-tone system of Bena-Yungur with an opposition between H, M and L must result from a relatively recent process of tonogenesis in which L tones were reinterpreted as M whenever they were not realised extra low due to a preceding voiced stop that acted as a depressor consonant. Although subsequent changes have somewhat blurred the correlation between tones and segments, this correlation still proves highly relevant for the internal reconstruction of the laryngeal settings of stem-initial consonants. We also show that the contemporary Bena-Yungur lexical tone patterns are the result of the neutralisation of a higher number of previously existing patterns due to the application of tone rules. The former distinctions between different tone patterns are still observable in the genitive construction for nouns and in positive perfective forms and product nominalisations for verbs. This allows us to reconstruct the original tone patterns of nouns and verbs, as well as aspects of the genitive construction and perfective verb forms. Remarkably, the tonal reconstruction makes it clear that the direction of tonal interactions must have shifted from anticipatory to perseveratory in the history of Bena-Yungur.