Heterotopic bone growth is a common finding after partial foot amputation that can predispose to recurrent wounds, osteomyelitis, and reamputation. Heterotopic ossification is the formation of excessive mature lamellar bone in the soft tissues adjacent to bone that is exacerbated by trauma or surgical intervention. The relevance of heterotopic ossification is dependent on its anatomic location. Its occurrence as a sequela of partial foot amputation can lead to prominence on the plantar aspect of the foot that can predispose the patient to recurrent neuropathic ulceration or preclude appropriate wound healing. Reulceration puts the high-risk patient who has already undergone local amputation at greater risk of recurrent infection and further amputation. The present study aimed to assess the incidence and risk factors for heterotopic ossification to further evaluate its role in partial foot amputation. A retrospective analysis of 72 consecutive patients who had undergone partial metatarsal resection was performed, with 90% of the cohort having peripheral neuropathy and 88% diabetes mellitus. Our findings revealed a heterotopic ossification incidence of 75% diagnosed radiographically. The initial onset of heterotopic ossification was not appreciated >10 weeks postoperatively. Ten patients (18.5%) exhibited heterotopic ossification-associated ulceration. The incidence of heterotopic ossification was 30% less in patients with peripheral vascular disease. These results indicate that heterotopic ossification is a common sequela of partial ray resection in an already high-risk patient population. The perioperative use of pharmacologic or radiation prophylaxis in an attempt to minimize amputation-related morbidity should be considered.