Drosophila melanogaster blue cheese (bchs) encodes a large BEACH (Beige and Chediak-Higashi) family protein that is postulated to function as an adaptor protein with roles in vesicle trafficking. Mutation in bchs leads to the accumulation of ubiquitinated aggregates in aged brains, presumably because of a conserved function with its human homologue Autophagy-Linked FYVE (ALFY), which interacts with Atg5 and p62 to promote the clearance of aggregate-prone proteins. In this study, we present pharmacological and genetic evidence using a well-defined larval motorneuron paradigm that in Drosophila bchs mutants, autophagic deficit contributes to neurodegeneration. Specifically, we show that motorneuron death in larvae is accompanied by the accumulation of prominent ubiquitinated aggregates in synaptic termini, and that these are sensitive to autophagy modulating drugs. In primary bchs neurons, early autophagic compartments increase in number and intensity based on Atg5 expression, but fail to progress to Atg8-labelled compartments, indicating non-clearance. A rescuing transgene encoding the longest Bchs BEACH domain isoform not only reverses this defect, but also greatly increases Atg8 compartment number and rescues neuronal death. Although only a small fraction of Bchs colocalizes with these markers under wild-type conditions, the population of Bchs that does associate with autophagosomes shuttles between different locations depending on how autophagy is induced. These observations, together with epistatic relationships between bchs mutant alleles and autophagy-modulating drugs and genetic backgrounds, points to a model whereby BEACH domain isoforms of Bchs participate in the early steps of autophagy by recruiting Atg5 to target substrates for clearance, and that Bchs' association with different parts of the autophagy machinery depends upon the type of autophagic stress imposed upon the neuron.