Previous studies have indicated that mothers of children at increased risk of type 1 diabetes (T1D) may modify their child’s diet following risk notification. Our aim was to investigate the diet quality after notified of T1D risk in at-risk children compared to not-at-risk children. The quality of nutrient intake (PANDiet score) and food intake (analyzed by a newly developed score and the HuSKY score) were assessed using three-day dietary records collected for at-risk children (BABYDIET study, n = 109) and a matched sample of not-at-risk children (DONALD study, n = 205) at nine and 24 months of age. Nutrient and food intake quality were lower at nine months of age and food intake quality was lower at 24 months of age in at-risk than in not-at-risk children (p = 0.01 and p