Long- and post-COVID syndrome (PCS) affect at least 65 million individuals globally, with an estimated incidence of 10% among over 651 million documented cases of SARS-CoV-2 infection. PCS impacts nearly every organ system, posing significant challenges for healthcare systems and patients. Despite this, effective guidelines for multimodal training or rehabilitation remain absent. The app-based physical intervention for long- and post-COVID treatment (A PILOT) study is a prospective, multicentre, two-armed, randomised controlled trial to evaluate the effectiveness of an app-based multimodal training intervention in patients with PCS. 100 participants will be randomly assigned to an intervention group (IG) or a control group (CG). Over 2 months, the IG will follow a standardised app-based intervention programme incorporating breathing exercises, endurance and strength training and progressive muscle relaxation. The CG will adhere to general WHO exercise recommendations during the waiting period and gain access to the app after the study concludes. Comprehensive assessments, including physical examinations, blood tests, psychological questionnaires, transthoracic echocardiography, electrocardiography and cardiopulmonary exercise testing, will be conducted pre- and post-intervention. The primary endpoints are the effects of app-based multimodal training on physical performance, neurocognitive function and health-related quality of life. Secondary endpoints include mental health outcomes (eg, depression, perceived stress, sleep quality and daytime sleepiness), echocardiographic and anthropometric measures and alterations in inflammatory markers and metabolites of the kynurenine pathway. This study aims to provide critical insights into structured app-based programmes, potentially establishing a framework for improving recovery in PCS patients.