Objectives This study aimed to analyse the relationship between adverse pregnancy outcomes (APO) and occlusal traits in the primary dentition, checking for different mediation paths. Setting and Sample Population Children evaluated at birth (T1), between 12 and 24 months (T2), and between 24 and 36 months (T3) were included. Two hundred and seventeen children who participated in T1 and T2 were randomly selected to perform the occlusion examination. Materials and Methods This is a prospective cohort study (BRISA). The theoretical model was tested by structural equation modelling (SEM), estimating standardized coefficients (Coeff.) (α = 0.05). The primary exposure was APO—a latent variable manifested from three health problems at birth: low birthweight (LBW), pre‐term birth (PTB) and intrauterine growth restriction (IUGR), evaluated in T1. The outcomes were four different occlusal traits assessed in T3: overjet, anterior and posterior crossbite, and crowding. Each outcome's direct and indirect effects were tested, mediated by growth, breathing, breastfeeding, and pacifier use. Results There was no direct association between APO and any of the outcomes: overjet (Coeff. = −0.163, P = .241), anterior crossbite (Coeff. = −0.696, P = .065), posterior crossbite (Coeff. = −0.087, P = .589) and crowding (Coeff. = 0.400, P = .423). The indirect (total and specifics) effects tested also showed no association (P > .05). However, APO was associated with lower child growth in all models; breastfeeding was associated with higher child growth in all models, and pacifier use was associated with overjet (Coeff. = 0.184, P < .001) and posterior crossbite (Coeff. = 0.373, P = .011). Conclusion APO was not a risk factor for overjet, crossbite and crowding in an early stage of the primary dentition by direct and indirect pathways. However, growth has been lower in children with APO and higher in children breastfed. Also, the harmful effects of using a pacifier in dental occlusion are highlighted.