Background <p>Nonunion is a common complication following foot and ankle arthrodesis. This study endeavoured to determine the risk factors for nonunion in foot and ankle arthrodesis.</p> Methods <p>This was a retrospective case–control study using the National Health Insurance Research Database. Patients who underwent foot and ankle arthrodesis with a minimum follow-up duration of 6 months were included. <i>International Classification of Diseases</i> codes were used to identify diagnoses and treatment. Patients with nonunion were matched by age and sex with patients with union at a ratio of 1:4. Logistic regression was performed to compare between patients with nonunion and controls with union to ascertain the effects of various risk factors.</p> Results <p>A total of 107 joints were identified as nonunion, and 428 age- and sex-matched controls were selected. Patients with diabetes mellitus had a 1.710 times (95% CI = 1.060 − 2.756, <i>p</i> = 0.0278) higher risk of nonunion than those without. No significant differences were observed in the risk of nonunion in relation to which joint was treated; the presence of osteoarthritis, traumatic osteoarthritis, rheumatoid arthritis, osteoporosis, or open/arthroscopic arthrodesis; internal or external fixation; or the usage of a bone graft. For patients without diabetes mellitus, those who underwent arthrodesis in the tarsometatarsal joint had a 6.507 times (95% CI: 1.045 − 40.522, <i>p</i> = 0.0256) higher risk of nonunion compared to those who underwent arthrodesis in the ankle joint.</p> Conclusion <p>Diabetes mellitus increases the risk of nonunion among patients with and without diabetes mellitus. For those without diabetes mellitus, arthrodesis in the tarsometatarsal joint is associated with the highest risk of nonunion.</p>