Flaxseed flour has been described as an excellent alpha-linolenic acid source. This study was designed to evaluate the effects of flaxseed flour on body adiposity and bone health in rats fed a flaxseed flour diet during lactation until 90 days. At birth, male Wistar rats were randomly assigned to control (C) and experimental (FF) groups, whose dams were treated with a control or flaxseed flour diet, respectively, during lactation. At 21 days, pups were weaned and fed a control and experimental diet until 90 days. Food intake, body mass and length were evaluated during a 21–90 day period. At 90 days, composition by dual-energy X-ray absorptiometry, serum hormonal profile, intra-abdominal fat mass, and lumbar vertebra and femur analyses was determined. Differences were deemed significant at p < 0.05. The FF group displayed the following (P < 0.05): a higher total lean mass (+7%), a lower total (−16%) and intra-abdominal (−24%) fat mass, a smaller adipocyte area (−30%), a higher femoral mass (+5%), bone mineral density (+5%) and radiodensity (+20%), and a higher maximum force (+10%) and breaking strength (+11%). The flaxseed flour diet displayed functional properties related to body growth maintenance associated with a lower risk of developing metabolic alterations, obesity and bone fragility.