Although breast milk is the normative feeding for infants, breastfeeding rates are lower than recommended. We investigated breastfeeding difficulties experienced by mothers in the first months after delivery and their association with early breastfeeding discontinuation. We conducted a prospective observational study. Mothers breastfeeding singleton healthy term newborns at hospital discharge were enrolled and, at three months post-delivery, were administered a questionnaire on their breastfeeding experience. Association among neonatal/maternal characteristics, breastfeeding difficulties and support after hospital discharge, and type of feeding at three months was assessed using multivariate binary logistic regression analysis. We enrolled 792 mothers, 552 completed the study. Around 70.3% of mothers experienced breastfeeding difficulties, reporting cracked nipples, perception of insufficient amount of milk, pain, and fatigue. Difficulties occurred mostly within the first month. Half of mothers with breastfeeding issues felt well-supported by health professionals. Maternal perception of not having a sufficient amount of milk, infant’s failure to thrive, mastitis, and the return to work were associated with a higher risk of non-exclusive breastfeeding at three months whereas vaginal delivery and breastfeeding support after hospital discharge were associated with a decreased risk. These results underline the importance of continued, tailored professional breastfeeding support.