Pregnancy is a period that is characterized by several metabolic and physiological changes and requires special attention, especially with regard to the relationship between feeding and fetal development. Therefore, the objective of this study is to evaluate whether the practice of voluntary physical exercise in combination with chronic consumption of fructose from the beginning of life and/or until the gestational period causes biochemical and genotoxic changes in pregnant females and in their offspring. 70 Swiss female mice received fructose in the hydration bottle and/or practiced voluntary physical exercise (VPE) for 8 weeks (pre-pregnancy/pregnancy). After the lactation period, the offspring groups were separated by sex. It was observed that the consumption of fructose affected the food consumption, serum concentration of fructose and glycemic profile in the mothers and that the VPE decreases these parameters. In addition, fructose was genotoxic in the mothers’ peripheral tissues and VPE had a preventive effect on these parameters. The offspring showed changes in food consumption, serum fructose concentration and body weight, in addition to an increase in the adiposity index in male offspring in the FRU group and a decrease in the FRU+VPE group. Fructose lead to hepatic steatosis in the offspring and VPE was able to decrease the area of steatosis. In addition, fructose led to genotoxicity in the offspring and VPE was able to modulate this effect, reducing damages. In conclusion, we observed that all interventions with voluntary physical exercise had nutritional, genetic and biochemical benefits of the mother and her offspring.