Although COVID-19 is being disruptive to all children, the effects are stronger for children with disabilities. Therefore, the aim of this study was to analyse, from a holistic perspective, the well-being of children with special needs during the total lockdown period in Spain. The 'Well-being of Children in Lockdown' (WCL) scale was completed by 1225 parents of which 3.1% (n = 38) had children with special needs. The results reveal the emergence of negative emotions among children with special needs, who were found to be crying more, feeling more nervous than usual, getting more angry and feeling sadder. These children also have more unhealthy habits, eat more than usual, overuse new technology and watch too many TV. Children with special needs scored lower for general well-being than those without these needs, and scored lower also for emotional aspects, playful and creative activities and physical activity.