Several healthcare processes, including rehabilitation, require prompt initiation and cannot be interrupted. Therefore, these processes underwent important adaptations during the COVID-19 pandemic. However, it is not fully known how healthcare facilities adapted their strategies and what the results were. This study investigated how rehabilitation services were affected during the pandemic and what strategies were employed to maintain the provided services. From June 2020 to February 2021, 17 semi-structured interviews were conducted with healthcare professionals working in rehabilitation services from the Brazilian Unified National Health System (SUS), who work at one of the three levels of care, in the municipalities of Santos and São Paulo, state of São Paulo, Brazil. The interviews were recorded, transcribed, and analyzed via content analysis. The professionals reported organizational changes in their services, with the initial interruption of appointments and, subsequently, the adoption of new sanitary protocols and the gradual return to in-person and/or remote appointments. Working conditions were directly impacted, as there was a need for staffing, training, increased workloads, as well as physical and mental exhaustion among professionals. The pandemic caused a series of changes in healthcare services, some of which were interrupted due to the suspension of numerous services and appointments. Some in-person appointments were maintained exclusively for patients who presented a risk of short-term deterioration. Preventive sanitary measures and strategies for continuity of care were adopted.