Mothers practice co-sleeping and breastfeeding simultaneously, for convenience and to strengthen bonding. Due to the scarcity of studies analyzing the impact of co-sleeping on primary dentition, this study aimed to analyze the possible effects of co-sleeping on children’s occlusion. In this cross-sectional study, mothers of 221 children aged 2–5 years who had been breastfed for less than 6 months completed a questionnaire about non-nutritive sucking habits. The WHO (World Health Organization) and IOTN-AC indices (the Aesthetic Component of the Index of Orthodontic Treatment Need) were used to assess malocclusion. The type of sagittal (dental and skeletal), transverse and vertical malocclusion was recorded. The non-co-sleeping group showed significantly higher pacifier use (p < 0.05), digital sucking (p < 0.05) and atypical swallowing (p < 0.05) habits. The non-co-sleeping group showed significantly higher mean scores on the IOTN-AC (p < 0.05) and WHO (p < 0.01), a significantly higher presence of canine class II (p < 0.05), anterior open bite (p < 0.05), posterior crossbite (p < 0.05), overbite (p < 0.05), skeletal class II (p < 0.01) and protrusion (p < 0.05). In conclusion, children who practice co-sleeping appear to have a lower frequency and duration of non-nutritive sucking habits. Co-sleeping may contribute to a lower development of malocclusions in children who are weaned early (before six months of age).