The information that can possibly be encoded in a given vocalization is limited by the available acoustic space. Vocalizations composed of several elements have the potential to distribute information among distinct elements and thus encode various layers of information simultaneously. Correspondingly, the multiple messages hypothesis states that different elements of a vocalization convey different information, for example, about identity, signallers’ quality or external events, which is directed to one or several receivers. The isolation call of the greater sac-winged bat, Saccopteryx bilineata, is a complex vocalization composed of different syllable types (variable, composite and stereotyped syllables). Pups produce isolation calls to elicit maternal care. In contrast to most bats, isolation calls of S. bilineata remain part of the adult vocal repertoire. In this study, we investigated the acoustic trajectories of isolation calls during ontogeny. Our analyses demonstrated that ontogenetic changes of acoustic parameters were most pronounced in stereotyped syllables. Throughout ontogeny, stereotyped syllables became shorter in duration and higher in frequency and bandwidth, thus effectively encoding information about age. Additionally, former studies revealed that composite syllables encode both an individual and a group signature. In our study, we also found an individual signature, thus corroborating the previous study. We conclude that isolation calls of S. bilineata encode multiple messages which are temporally segregated. The composite syllables conveyed information about individual identity and social group affiliation, whereas the stereotyped syllables encoded information about age. The temporal segregation allows the separation of information conveyed by distinct elements, thus enhancing signal reliability.