Background: The COVID-19 pandemic has had wide-reaching primary and secondary health implications. The UK government implemented a national lockdown to slow the rate of infection at the end of March 2020, lasting until early summer 2020. The results from a UK nationwide survey suggest the majority of inflammatory bowel disease patients were followed up using technology-enabled care services (TECS) during this time. We therefore aimed to explore the impact of the pandemic on nutritional status of children with inflammatory bowel disease, focusing on the effect of national lockdown from March to early summer 2020. Methods: A retrospective study was conducted. All patients with a diagnosis of inflammatory bowel disease, aged <18 years, and under the care of Southampton Children's Hospital were eligible for inclusion. Those patients who attended an outpatient appointment during time period 1 (November 2019 to February 2020), and following the period of national lockdown, time period 2 (July to November 2020), were included in the analysis. Results: In total, 116 patients had paired measures. Using the World Health Organization criteria of nutritional status, 19% (n = 22/116) were mildly malnourished with a body mass index Z score (BMIZ) < -1. In this group, the mean BMIZ was -1.3 ± 0.9 at time point 1 versus -1.9 ± 0.9 at time point 2 (p = 0.03). The mean BMIZ score of those children who were overweight at time point 1 was 1.2 ± 1.2 versus 1.6 ± 1.4 at time point 2 (p = 0.2) During the period of lockdown, 27% of malnourished children (n = 6/22), 2% of normally nourished children (BMIZ > -1 to < 1) (n = 1/51) (p ≤ 0.0001) and none of the overweight children (BMIZ > 1) (n = 0/43) children (p ≤ 0.0001) had a TECS nutrition review. Conclusions: Dietetic reviews were severely restricted during the first national lockdown. Patients with low BMIZ prior to lockdown became more malnourished. During the ongoing pandemic, it is important to identify those children with nutrition risk, focusing support on this group of children.