The contribution of paternal obesity to pregnancy outcomes has been little described. Our aims were to determine whether the effect of an antenatal maternal dietary and lifestyle intervention among women who are overweight or obese on newborn adiposity, was modified by paternal obesity. We conducted a secondary analysis of a multicenter randomised trial. Pregnant women with BMI ≥25 kg/m2 received either Lifestyle Advice or Standard Care. Paternal anthropometric measures included height, weight, BMI; waist, hip, calf and mid-upper arm circumferences; biceps and calf skinfold thickness measurements (SFTM); and percentage body fat. Newborn anthropometric outcomes included length; weight; head, arm, abdominal, and chest circumferences; biceps, triceps, subscapular, suprailiac, thigh, and lateral abdominal wall SFTM; and percentage body fat. The effect of an antenatal maternal dietary and lifestyle intervention among women who were overweight or obese on neonatal anthropometric measures, was significantly modified by paternal BMI ≥35.0 kg/m2, with a significantly smaller infant triceps, suprailiac, and thigh SFTM, and percent fat mass, compared with that observed in offspring of lean fathers. Further research is required to determine whether our observed associations are causal, and whether paternal weight loss prior to conception is a potential strategy to reduce the intergenerational effects of obesity.