Heterotopic ossification (HO) is the formation of extraskeletal bone in muscle and soft tissues and could be genetic or non-genetic. The classic presentation of non-genetic HO is in young adults with a clear history of local trauma, surgery or prolonged immobilization after spinal cord and traumatic brain injuries. Genetic HO has a significant clinical severity compared to non-genetic causes and includes fibrodysplasia ossificans progressiva (FOP). FOP is an extremely rare genetic skeletal disorder characterized by congenital malformations of the great toes and progressive heterotopic ossification that forms qualitatively normal bone in characteristic extraskeletal sites affecting skeletal muscles, fascia, tendons, and ligaments. Previously, it has been reported an association between SARS-CoV-2 infection (COVID-19) and HO or FOP exacerbation with unclear etiopathogenesis. The possible mechanisms could be prolonged immobilization and systemic inflammation. Here, we describe the case of a 55-year-old apparently healthy man who suffered from a severe SARS-CoV-2 infection after that he experienced an extensive and progressive heterotopic ossification around the shoulders, the elbows, the hip, the knees, and the ankles. Because of the clinical severity, the painful soft-tissue swelling, the progressive HO, and the bilateral congenital hallux valgus deformity, a late-onset atypical FOP was suspected. Nevertheless, no variant of clinical significance has been identified in the coding regions and splicing sites in the ACVR1 gene and no deletions and/or duplications have been identified in exonic regions.