The aim of this study was to determine the flavonoid profile of Lupinus mexicanus germinated seed extract (PE) and to evaluate its effect as a phytoestrogen on the morphometric parameters of CA3 hippocampal neurons of ovariectomized rats (OVX). L. mexicanus seeds, germinated for 48 h, were homogenized and macerated using an 80% ethanol solution. The extract was analyzed by HPLC/MS-MS. Thirty young Wistar strain female rats (200±10 g) were randomly distributed into four groups: sham operated (S) treated with dimethyl sulfoxide (vehicle); ovariectomized and treated with 1250 μg of PE extract (OVX-PE); ovariectomized and treated with 5 μg estradiol benzoate (OVX-EB); and ovariectomized and vehicle treated (OVX). All substances were injected subcutaneously daily for 28 days. On day 29, the animals were sacrificed, perfused, and fixed to obtain the brains for histological processing. Each brain was cut and stained with hematoxylin and eosin. The thickness of the stratum oriens (SO), the nuclear diameter, and the neuronal density were measured in the hippocampus CA3 area. Nine different flavonoids and one non-identified compound were detected. The histological analysis demonstrated that the thickness of the SO was higher in the OVX-EB and S groups than in the OVX-PE and OVX groups (p⟨0.05); in addition, the nuclear diameters of the neurons in the OVX-EB and S groups were higher compared with the other groups (p⟨0.05). The OVX group had the highest cellular density among groups (p⟨0.05). Based on our results, the PE obtained did not have beneficial effects on CA3 hippocampal neurons.