Dysautonomia in the post-COVID-19 condition appears to affect a significant number of patients, with reports raising the incidence up to 61%, having an overlap with myalgic encephalomyelitis/chronic fatigue syndrome. Quality of life and daily function are significantly impacted and conservative management interventions, despite the lack of high-quality evidence to date, are needed to ameliorate disability. A total of 50 adults with a dysautonomia post-COVID-19 diagnosis based on the Ewing battery and a NASA lean test will be enrolled in a randomized single blinded controlled trial with a crossover design. Feasibility and lack of definite dysautonomia diagnosis will be the primary outcomes, while secondary outcomes will be health-related, clinical and cardiopulmonary exercise test indicators. Safety and acceptance will also be checked, primarily excluding participants with post-exertional malaise. The Long-COVID patients Causal Diagnosis and Rehabilitation study in patients with Dysautonomia (LoCoDiRE-Dys) intervention will consist of an educational module, breathing retraining and an individualized exercise intervention of biweekly sessions for two months with regular assessment of both groups. LoCoDiRe-Dys aims to be the first post-COVID-19 randomized study in people with dysautonomia offering a multimodal intervention both in diagnosis and management. The need for evidence in effectively supporting patients is eminent.