Non-standard work schedules (NSWS) have become typical, but their associations with childcare arrangements and children's well-being are unknown. This study explores how risk factors are associated with the social–emotional well-being of girls and boys using flexibly scheduled early childhood education and care. Furthermore, the study investigates whether well-functioning cooperation between parents and educators buffers the negative effects of the risk factors. This study, which is a part of a larger survey carried out in three European countries, reports Finnish parents' (N = 146) perspectives. The results showed that high parental stress was associated with low child well-being. Strong parent–educator cooperation positively impacted both boys' and girls' social–emotional well-being. The risk factors of reconciling work and family life had negative associations with children's well-being and the fulfilment of their basic needs. The results illustrate the complex interrelations between children's well-being, risk factors relating to NSWS and the buffering effect of protective factors.