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Background Few studies have examined the burden of post-acute sequelae of coronavirus disease 2019 (COVID-19) (PASC) in low- and middle-income countries (LMICs). We sought to characterize PASC with self-reported questionnaires and clinical examinations of end-organ function in Lima, Peru. Methods From January to July 2021, we recruited participants at least eight weeks after COVID-19 diagnosis from a case registry in Lima, Peru. We evaluated participants for PASC with questionnaires, neuropsychiatric evaluations, chest X-ray, spirometry, electrocardiogram, and echocardiogram. We used multivariable models to identify risk factors for PASC. Results We assessed 989 participants for PASC at a median 4.7 months after diagnosis. Clinically significant respiratory symptoms were reported by 68.3% of participants, particularly those who had been severely ill during acute COVID-19, and were associated with cardiac findings of ventricular hypertrophy or dilation on echocardiogram. Neuropsychiatric questionnaires were consistent with depression in 20.7% and cognitive impairment in 8.0%. Female sex and older age were associated with increased risk of respiratory (aOR 2.36, 95% CI 1.69 to 3.31; aOR 1.01, 95% CI 1.00 to 1.03, respectively) and neuropsychiatric sequelae (aOR 2.99, 95% CI 2.16 to 4.18; aOR 1.02, 95% CI 1.01 to 1.03, respectively). Conclusions COVID-19 survivors in Lima, Peru experienced frequent post-acute respiratory symptoms and depression, particularly among older and female participants. Clinical examinations highlighted the need for cardiopulmonary rehabilitation among persons with severe COVID-19; psychosocial support may be required among all COVID-19 survivors.