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Abstract Background Long COVID is suggested to be present in 14 to 43% of COVID 19-survivors. Literature on this new condition states a need for a multidisciplinary approach including physical exercise and nutrition. The aim of the current pilot study is to investigate the feasibility of the proposed protocol to prepare for a randomized controlled study that addresses the effectiveness of a personalized multimodal treatment compared to standard physiotherapy. Methods This is a protocol of the UNLOCK (Nutrition and LOComotoric rehabilitation in long COVID) study, a pragmatic, single center, randomized controlled pilot trial with two groups. Patients with persisting symptoms related to a SARS-CoV-2 infection will receive either standard physiotherapy or a personalized multimodal treatment for a period of 12 weeks, consisting of individualized physical exercise program combined with individualized nutritional therapy. They will be followed-up at 6, 12, and 18 weeks after randomization. Discussion A multidisciplinary approach for dealing with long COVID is needed. Because of the lack of clear data and the fact that this is a very heterogenic group, we aim to prepare and optimize a randomized controlled study that addresses the effectiveness of a personalized multimodal treatment. Trial registration ClinicalTrials.gov Identifier: NCT05254301 (since February 24, 2022).