In women, bone mass undergoes changes during pregnancy and the postpartum period, which has a risk for subsequent development of osteoporosis. Thus, the present study aims to evaluate the effects of flaxseed flour in femur quality during post-weaning of dam rats. After weaning, the rats were divided into control (C, n = 7) and experimental (F, n = 7) groups treated with a diet containing 25 g of flaxseed flour in the lactating period and 15 g in the maintenance period. After 51 days post-partum, serum hormone, fatty acids composition, bone compartments, computed tomography, and biomechanical analyses were determined. Food intake, length, body mass, hormone analysis, and total bone compartments showed similar results. For biomechanical and computed tomography analysis and fatty acids composition, the F group showed higher maximum force (+12%, p < 0.05), breaking strength (+25%, p < 0.05), rigidity (+17%, p < 0.0001), and femoral head radiodensity (+15%, p < 0.05) and presented lower total polyunsaturated fatty acids (-17%, p < 0.0001) and arachidonic acid (-44%, p < 0.0001) and higher ALA (+695%, p < 0.0001) and EPA (+160%, p < 0.05). Fatty acids composition of flaxseed flour, as well as its protein profile and calcium content, were able to improve the bone quality, which may be associated with lower serum levels of arachidonic acid and higher EPA, showing an anti-inflammatory profile and increased deposition of organic matrix during the post-weaning period, and may result in prevention of future osteoporosis.