Malnutrition is associated with poor functional performance in geriatric rehabilitation inpatients. However, it is unclear if malnourished patients have poor functional trajectories over time. This study aimed to determine the association between (the risk of) malnutrition at admission and trajectories of Activities of Daily Living (ADL) and Instrumental ADL (IADL) from pre-admission to post-discharge in geriatric rehabilitation inpatients. An observational, longitudinal study was conducted in the REStORing health of acutely unwell adulTs (RESORT) cohort of geriatric rehabilitation inpatients. A total of 618 patients (mean age 82.1 ± 7.8 years, 57.4 % females) were included. The prevalence of the risk of malnutrition, by Malnutrition Screening Tool (MST) was 41.3 % (n = 255) and malnutrition by the Global Leadership Initiative on Malnutrition (GLIM) and European Society for Clinical Nutrition and Metabolism (ESPEN) criteria were 53.5 % (n = 331) and 13.1 % (n = 81) respectively. Malnutrition by the GLIM criteria but not the ESPEN criteria nor the risk of malnutrition, was associated with ADL trajectories of ‘remained poor’ (OR: 3.33, 95 %CI: 1.21−9.19) and ‘deteriorated’ (OR: 1.68, 95 %CI: 1.13−2.52) compared to the ‘recovered’ trajectory. The risk of malnutrition and malnutrition were not associated with IADL trajectories. Malnutrition at admission was associated with poor ADL trajectories but not IADL trajectories in geriatric rehabilitation inpatients.