The COVID-19 pandemic negatively impacted mental health globally. Individuals with neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD), are at elevated risk of mental health difficulties. Therefore, we investigated the impact of the pandemic on anxiety, depression and mental wellbeing in adults with NDDs using longitudinal data from the Avon Longitudinal Study of Parents and Children study (n=3,058). Mental health data were collected pre-pandemic (age 21-25) and at three timepoints during the pandemic (ages 27-28) using the Short Mood and Feelings Questionnaire, Generalised Anxiety Disorder Assessment-7, and Warwick Edinburgh Mental Wellbeing Scale. ADHD and ASD were defined using validated cut-points of the Strengths and Difficulties Questionnaire and Autism Spectrum Quotient, self-reported at age 25. We used multi-level mixed-effects models to investigate changes in mental health in those with ADHD and ASD compared to those without. Prevalences of depression, anxiety and poor mental wellbeing were higher at all timepoints (pre-pandemic and during pandemic) in those with ADHD and ASD compared to those without. Anxiety increased to a greater extent in those with ADHD (β=0.8 [0.2,1.4], p=0.01) and ASD (β=1.2 [-0.1,2.5], p=0.07), while depression symptoms decreased, particularly in females with ASD (β=-3.1 [-4.6,-1.5], p=0.0001). On average, mental wellbeing decreased in all, but to a lesser extent in those with ADHD (β=1.3 [0.2,2.5], p=0.03) and females with ASD (β=3.0 [0.2,5.9], p=0.04). To conclude, anxiety disproportionately increased in adults with NDDs during the pandemic, however, the related lockdowns may have provided a protective environment for depressive symptoms in the same individuals.