Interactions between microbial symbionts of metazoan hosts are emerging as key features of symbiotic systems. Little is known about the role of such interactions on the maintenance of symbiosis through host’s life cycle. We studied the influence of symbiotic bacteria on the maintenance of symbiotic yeast through metamorphosis of the fly Drosophila melanogaster . To this end we mimicked the development of larvae in natural fruit. In absence of bacteria yeast was never found in young adults. However, yeast could maintain through metamorphosis when larvae were inoculated with symbiotic bacteria isolated from D. melanogaster faeces. Furthermore, an Enterobacteriaceae favoured yeast transstadial maintenance. Because yeast is a critical symbiont of D. melanogaster flies, bacterial influence on host-yeast association may have consequences for the evolution of insect-yeast-bacteria tripartite symbiosis and their cooperation.