We report a hitherto unprecedented diversity of fly larvae (Diptera) from Eocene Baltic amber and the use of these to address palaeo-ecosystem functions and processes in the surrounding forests. Fly larvae have been considered exceptionally rare by the research community and have, like most insect larvae, been deemed of limited utility owing to challenges in identification. Herein, however, using synchrotron-x-ray radiation CT (SR-µCT) allowed us to detect and identify dozens of fly larvae from Baltic amber, and to infer their ecological interactions. One particular piece of amber contains 56 fly larvae and apparent mammalian feces. This fossil is of great interest for our understanding of carbon cycling in the Eocene forest. The occurrence of such a large number of fly larvae on the fecal remains indicates an important role of flies in recycling organic matter in the Eocene forest, much as some larvae do today. Analysis of the fly palaeo-communities also allowed us to hypothesize a mechanism by which massive, geologically relevant deposits of amber were formed in the Baltic region. Scanning allowed us to identify seven larvae closely related to the extant Syrphidae, whose larvae inhabit nests of eusocial Hymenoptera, or, sometimes, flows of sap dripping from trees damaged by other burrowing insect larvae.