Background: Periconceptional nutrition may have an important function in programming the immune function and allergies, however, there is a lack of studies assessing pre-conception food intake and childhood allergic disorders. The aim of the current study was to identify maternal pre-conception dietary components that may be associated with allergic disorders in children up to 3 years of age. Methods: Pregnant women attending their first antenatal visit and who were aged >18 years were invited to participate. Pre-conception food frequency data was retrospectively collected at 18 weeks’ gestation. Childhood eczema, current wheeze, and rhinitis was assessed at 36 months of age using a questionnaire and doctor diagnosis (n = 234). Linear discriminant analysis (LDA) was used to explore the combination of dietary food components that best discriminated between allergy status in children. Results: Maternal pre-conception food intake such as low and high fat dairy, fresh fruit, unsaturated spreads, and take-away foods, were protective for any allergy assessed. Non-oily fish was protective for eczema and current wheeze; saturated spreads (e.g., butter) was protective for eczema, current wheeze, and rhinitis; poultry and fruit juice were adversely associated with each allergy. Conclusions: Pre-conception food intakes demonstrate inconsistent and somewhat contrary relationships to the development of child allergies. Whether and how maternal food intake impacts the underlying fetal programming and the mechanisms of childhood allergy warrants further investigation.