Eczema and food allergy may impact diet. Using data from a cohort of Manitoba children born in 1995, we examined calcium intake, defined as the frequency and quality of calcium products consumed (with the exception of cheese), amongst Manitoba adolescents (12–14 years) with eczema or food allergy in childhood (7–8 years) or adolescence. At both ages, children were assessed by a physician for eczema and food allergy. Adolescents completed food frequency questionnaires. Calcium intake was defined as 1+ vs. <1 weekly. Linear and logistic regression was used as appropriate, with adjustments for confounders. Overall, 468 adolescents were included, of whom 62 (13.3%) had eczema only in childhood, 25 (5.3%) had food allergy only, and 26 (5.6%) had eczema and food allergy. Compared to children without eczema, those with eczema only had poorer calcium intake in adolescence (β −0.44; 95%CI −0.96; 0.00). Girls, but not boys, with eczema in childhood had poorer calcium intake in adolescence than girls without eczema (β −0.84; 95%CI −1.60; −0.08). These patterns persisted even if children experienced transient vs. persistent eczema to adolescence. Similar but non-significant trends were found for food allergy. Childhood eczema is associated with significantly lower calcium intake and consumption in adolescence. These differences persist to adolescence, even if a child “outgrows” their allergic condition.