This paper addresses nine open issues in the historical phonology of Mojeño, an Arawakan language of Bolivia. We propose solutions to these problems by postulating reconstructed forms for Proto-Mojeño based on a comparison of the two extant varieties of the language, Ignaciano and Trinitario, and on 17th century sources on Old Mojeño. Contrarily to a recent claim, we argue that the contrast between *n and *ɲ can be straightforwardly reconstructed for Proto-Mojeño. We suggest that the marginally contrastive opposition between s and ʃ in Ignaciano derives from sound symbolism. We argue for a contrast between *a and *o in Proto-Mojeño that was later lost in Ignaciano. We reconstruct the accentual system of Proto-Mojeño, as a basis for explaining diachronic rhythmic syncope in Trinitario. Syncope of vowels in weak metrical positions accounts for the emergence of consonant clusters and morphophonological alternations in Trinitario. Besides, hiatus resolution has led to the phonologization of the consonant /c/, while the vowel /ə͡e / emerged from a process of monophthongization. Indirect consequences of Trinitario rhythmic syncope are the phonologization of the consonant /ç/, consonant loss and the development of phonological vowel length. An appendix presents 190 Proto-Mojeño reconstructions and cognate sets.