Microsporidia are located at the base of the fungal evolutionary tree. They are obligate intracellular parasites and harness host metabolism to fuel their growth and proliferation. However, how the infestation of cells affects the whole organism and how the organism contributes to parasite proliferation remain poorly understood. Here, we have developed a Tubulinosema ratisbonensis systemic infection model in the genetically amenable Drosophila melanogaster host, in which parasite spores obtained in a mammalian cell culture infection system are injected into adult flies. The parasites proliferate within flies and ultimately kill their hosts. As commonly observed for microsporidia infecting insects, T. ratisbonensis preferentially grows in the fat body and ultimately depletes the host metabolic stores. We find that supplementing the fly diet with yeast does not benefit the host but the parasite, which increases its proliferation. Unexpectedly, fatty acids and not carbohydrates or amino acids are the critical components responsible for this phenomenon. Our genetic dissection of host lipid metabolism identifies a crucial compound hijacked by T. ratisbonensis: phosphatidic acid. We propose that phosphatidic acid is a limiting precursor for the synthesis of the parasite membranes and, hence, of its proliferation.