Within many cellular organelles biochemical functions are compartmentalized, which facilitates optimized enzymatic environments. However, processing and or storage of metabolites in the same pathway can occur in multiple organelles. Thus, spatially separated organelles would need to cooperate functionally. Coordination would also be needed between organelles in different specialized cells, with shared metabolites passed via circulation. Peroxisomes are membrane-bounded organelles responsible for cellular redox and lipid metabolism in eukaryotic cells. Studies using single cells suggest peroxisomes coordinate with other organelles including mitochondria, ER (endoplasmic reticulum), lysosomes, and lipid droplets. Some of these coordinated functions require, or are at least enhanced by, direct contact between peroxisomes and other organelles. Peroxisome dysfunction in humans leads to multiorgan effects including neurological, metabolic, developmental, and age-related diseases. Thus, increased understanding of peroxisome coordination with other organelles, especially those specialized cells in various organs is essential. Drosophila melanogaster (fruit fly) has emerged recently as an effective animal model for understanding peroxisomes. Here we review current knowledge of genetic pathways regulating coordination between peroxisomes with other organelles in flies, speculating about analogous roles for conserved Drosophila genes encoding proteins with known organelle coordinating roles in other species.