In the wide distribution range of the red squat lobster Pleuroncodes monodon in the Southeast Pacific Ocean, there is an important nursery area on the southern coast of Chile. The new juvenile individuals from this nursery area are directly recruited into the adult squat lobster population, which is exploited by industrial fisheries. Despite the importance of new P. monodon juveniles for recruitment estimations in fishery management models, their bioenergetic condition and/or nutritional status at the onset of their benthic phase remain unknown, as are the differences in the biochemical composition and energy reserves of the two sexes, which could help explain the cost of the first breeding event in females. Therefore, in new juvenile squat lobsters with the same degree of immaturity, we quantified and compared between the sexes (female vs. male): the size (cephalothorax length, CL), body biomass (dry weight and organic matter), biochemical composition (proteins, glucose, and lipids), and fatty acid profiles (FAs). The results indicate that the CL of new juveniles was similar between the sexes, while the dry weight and organic matter presented significant differences, with higher values in new juvenile females (NJF) than new juvenile males (NJM). Similarly, the NJF had a higher content of proteins, glucose, and lipids than NJM. The FAs also showed significant differences between the sexes; the NJF had a higher content than NJM in all fatty acid classes (i.e., saturated, monounsaturated, and polyunsaturated), with the FAs DHA (C22:6n‐3), EPA (C20:5n‐3), oleic (C18:1n‐9), palmitic (C16:0), and eicosatrienoic (C20:3n‐3) significantly contributing to the differentiation of FA profiles between the sexes. All of the aforementioned differences among the multiple variables of the bioenergetic condition can indicate biochemical adaptations in the storage capacity of energy reserves, particularly among NJF that must support the high energy cost of the first reproductive event (characterized by embryo production and incubation), which occurs during the austral winter, a period predominated by cold‐water temperatures and scarce food availability in the habitat. Overall, our findings have significant implications in fishery management models. In this case, defining the bioenergetic condition of the new juvenile squat lobsters can aid in predicting the density and stability of the adult population, which is exploited by commercial fisheries.