Purpose Knowledge gaps exist regarding the effects of interventions due to continuing respiratory symptoms in patients with post-COVID condition. The aim of the present study was to present the clinical outcomes of individualised treatments for patients with remaining respiratory symptoms due to post-COVID condition. Methods This prospective longitudinal study included a consecutive series of 57 patients with remaining respiratory post-COVID symptoms. Breathing pattern, thoracic pain/mobility, occurrence of cough, and respiratory muscle strength were assessed before and after the administration of individually tailored physiotherapy interventions. Results The median treatment duration was 3 months (range 1–36 months). Dysfunctional breathing pattern was the most common symptom (n = 55/57) at inclusion. After treatment, 95% of patients had a normalised or improved breathing pattern (p < 0.001). The treatments for pain, productive and unproductive cough, and respiratory muscle strength resulted in significantly improved symptoms (p < 0.01). With other targeted treatments, inspiratory muscle strength improved by 20 cmH2O and expiratory muscle strength by 11 cmH2O (both p < 0.001). Conclusions This study indicates positive outcomes of physiotherapy treatment based on the patient’s symptomatology and test results. Therefore, individualised physiotherapy treatment of post-COVID conditions may have an impact on recovery.