Background: Early research showed weight gain in children during the COVID-19 pandemic. Objective: To compare changes in BMI z-score of children with overweight and obesity in a personalised lifestyle intervention before and during the pandemic. Methods: Changes in BMI z-score half a year (T6) and twelve months (T12) after the first lockdown were included for 71 children in the ‘2020 during COVID’ group and compared to 48 children in the ‘2019 before COVID’ group, using a marginal model for repeated measures (model 1). Model 2 corrected for lifestyle intervention characteristics, and model 3 corrected additionally for family characteristics. Results: The mean difference in BMI z-score change was significantly different at T12 (+0.07 in 2020 versus −0.09 in 2019, p = 0.022). Model 3 showed significant differences in BMI z-score change at both T6 (+0.15, p = 0.024) and T12 (+0.18, p = 0.016). This model also defined ‘having a mother with obesity’ (+0.13, p = 0.019) and the frequency of no-show consultations (+0.41 per missed consultation per month, p = 0.025) as related factors. Conclusions: Lifestyle intervention in children with overweight and obesity is less successful in decreasing BMI z-score during the COVID-pandemic. Identified risk factors for less success could contribute to identifying children with higher risks for, and possibly prevent, BMI z-score increase.