Background and Objectives: According to recent physiotherapy recommendations (WHO, WCPT, 2020) for patients with COVID-19, after discharge from an ICU, they are expected to experience respiratory, physical, cognitive, and psychological problems due to the duration and nature of the immobilization and sedation, ventilation duration, and underlying morbidity. Moreover, only patients with a limitation in physical capacity and/or physical activity have an indication for physiotherapy. However, little is known about the effect of physiotherapy treatment on the functional capacity of patients with COVID-19. Purpose: The aim of the present study was to provide information for the effectiveness of physiotherapy intervention on the respiratory and physical functional status of patients with COVID-19, since there will be a great demand for physiotherapy treatment for these people soon. Materials and Methods: The Ethics Committee of the AHEPA University Hospital, School of Medicine, Health Sciences Faculty, Aristotle University of Thessaloniki, Greece granted approval for this study. This pilot clinical study was conducted from March to June 2020. The sample consisted of 11 patients with COVID-19, discharged from an ICU and hospitalized in the COVID-19 clinic of AHEPA University Hospital. All participants had an indication for physiotherapy, according to the recommendations, and a medical referral as well. The duration of their hospitalization ranged from two to six weeks. Among participants, there were seven males and four females, aged from 44–75 yrs, five smokers and six nonsmokers, four obese and seven nonobese. According to the recommendations, physiotherapy intervention was tailored to the patients’ needs and goals. Breathing exercises, early mobilization, and self-management for daily living were performed once a day, for five days a week, as tolerated. Measurement tools: Pulse oximeter (SpO2), respiratory rate (RR), the Borg scale (intensity of dyspnea), Medical Research Council scale for disability (MRCd), clinical evaluation for dysfunctional breathing (DB), Medical Research Council scale for muscle strength (MRCms), Berg balance scale, Sit to Stand test (leg strength and endurance), Time Up and Go test (TUG) (general mobility), 1 min walk test (1MWT) (aerobic capacity), and the Barthel Index (BI) (performance in daily activities). For the purposes of the study, two measurements were conducted: at admission and at discharge from the COVID-19 clinic. Results: Dependent sample tests showed a significant effect (p < 0.001) for the recommended physiotherapy treatment on respiratory variables: 6.9 (1.4)% for SpO2, 3.4 (0.9) breaths for respiratory rate, and 5.0 (1.3) for the Borg scale score. Significant improvements (p < 0.001) were additionally noted for physical functioning: 25.3 (13.0) for the Berg balance scale, 18.5 (11.2) for the MRCms score, 3 (1.3) s for the Sit to Stand test, 40.4 (40.6) s for the TUG efforts, 44.1 (25.5) s for 1MWT, and 65.9 (20.2) for BI. All patients displayed DB at admission to the COVID-19 clinic, while nine of them adopted a diaphragmatic breathing pattern at discharge. At admission to the COVID-19 clinic, all patients were at level five disability (MRCd), whereas at discharge 10 out of 11 patients improved (three at level four, four at level three, and three at level two). Conclusions: The present pilot study provided first evidence for the effectiveness of the WHO and WCPT physiotherapy recommendations on the respiratory and physical functioning status of patients with COVID-19. Further studies are needed to support these early findings.