The COVID-19 pandemic has had a huge impact on children’s lifestyle and eating behaviour, resulting in an increase of obesity prevalence. The CEBQ (Children’s Eating Behaviour Questionnaire) is a validate questionnaire that investigates children’s eating behaviour. Knowing the psychological consequences of daily routine disruption during lockdown, we evaluated the changes in eating behaviours in a paediatric cohort before and during the lockdown period through the evaluation of the Italian version of the CEBQ. We prospectively enrolled children attending the pediatric clinic of the University of Campania ‘Luigi Vanvitelli’. All parents answered the parent-report version of the CEBQ before lockdown containment. During lockdown, the second survey was carried out by telephone call. The study sample included 69 children. Food responsiveness and emotional overeating subscales showed higher scores during lockdown compared to data before lockdown (p = 0.009 and p = 0.001, respectively). Conversely, desire to drink and satiety responsiveness showed lower scores at follow-up (p = 0.04 and p = 0.0001, respectively). No differences were observed for slowness in eating and enjoyment of food. Delta changes were higher in normal-weight children compared to children with obesity (p = 0.02). Our results confirm that containment measures during the COVID-19 pandemic have acted as triggers on certain eating behaviors that mostly predispose to an obesogenic manner.