Individuals with persistent impairments due to Coronavirus disease 2019 (COVID-19) can receive pulmonary rehabilitation in Germany. To date, there is no evidence of the medium- or long-term effects of pulmonary rehabilitation on Long COVID. This study examined changes in health and occupational outcomes over time and described the therapeutic content of pulmonary rehabilitation and aftercare. This analysis also compared two rehabilitation groups after COVID-19 who had different levels of access to rehabilitation. Longitudinal observational study with multicenter and prospective data collection. Pulmonary rehabilitation in four different rehabilitation facilities in Germany. Individuals with a mild course of disease and long-lasting impairments (inpatient rehabilitation, IR) and patients with a severe course after hospitalization (follow-up rehabilitation, FuR). Participants had to be between 18 and 65 years of age. Written questionnaires were administered at the beginning and end of rehabilitation, as well as six and twelve months after rehabilitation. Health-related quality of life (HrQoL), fatigue, participation restrictions, COVID-19 symptoms, mental and physical health were assessed, as well as occupational outcomes and questions about rehabilitation and aftercare. IR patients were predominantly female (68.0%) and 52 years of age on average, while 66.1% of Long COVID rehabilitees in FuR were male and three years older. Over the course of rehabilitation, most COVID-19 symptoms decreased with statistical significance. The subjective health scales showed improvements with medium to large effect sizes (ES) over time in IR (P<0.01; ES between 0.55 (cognitive fatigue) and 1.40 (physical fatigue)) and small to large effects in FuR (P<0.01; ES between 0.45 (anxiety) and 1.32 (physical fatigue)). One year after rehabilitation, most effects remained at a moderate level. After twelve months, an increase in neurocognitive symptoms was observed in FuR patients. More than 80% of employed people returned to work one year after rehabilitation, although FuR patients returned to work a median of four weeks later (P<0.01). The comparative analysis showed that rehabilitees in different forms of rehabilitation attended rehabilitation with different impairments and rehabilitation goals, which are partly considered in treatment and aftercare. To provide needs-based rehabilitation to different rehabilitation groups with Long COVID, knowledge of their health histories and preferences is necessary.