The red squat lobster Pleuroncodes monodon is a species of high commercial value that inhabits the Humboldt Current System. Along the Chilean coast, two populations are exploited by the fishing industry, one located off the coast of Coquimbo and the other off the coast of Concepción. Yet, it is unknown whether there are differences in the “bioenergetic fuel” (measured as lipid content and fatty acid profile) of juvenile populations of these two fishing units and whether these bioenergetic compounds can be modulated by differences in the environmental parameters (such as temperature or chlorophyll-a) of their breeding areas. To shed some light on this, we measured the lipid content and fatty acid profiles of the viscera and muscle of juvenile female red squat lobsters from these two fishing units, specifically from breeding areas near long-exploited fishing grounds: a) the northern fishing unit (NFU, from 26°S to 30°S) and b) the southern fishing unit (SFU, from 32°S to 37°S). We found differences in the lipid content, fatty acid profiles, and ratios of saturated fatty acids (C16:0/C18:0) of juvenile females from these two locations. In addition, the essential fatty acids (DHA/EPA) found in the viscera versus the muscle of these lobsters varied significantly. Juvenile females from the SFU (i.e. Concepción) showed a higher lipid content compared to the juvenile females from the NFU (i.e. Coquimbo). Consistently, individuals from the SFU had a higher content of fatty acids, which also proved to be richer in saturated and monounsaturated fatty acids compared to those from the NFU. Our results are important for the fisheries in both areas because these juvenile populations are the source of new recruits for the adult populations that are exploited by the fishing industry. Our study also aids in determining which populations are healthier or of better quality in bioenergetic terms. Furthermore, increasing the incorporation of bioenergetic parameters in fishery models is essential for the recruitment and stock assessment within an ecosystem approach, since it allows for the evaluation of the nutritional condition of different fishing populations.