Background In African populations, estimated glomerular filtration rate by cystatin C (eGFRcys) is better aligned with gold-standard GFR measurements than eGFR by creatinine (eGFRcr). Moreover, eGFRcys is unaffected by the effects of antiretroviral therapy (ART) on tubular secretion and may thus provide better estimates of GFR in people with HIV on ART. Setting Observational cohort study of people of African ancestry living with suppressed HIV RNA on ART in London, United Kingdom. Methods Cross sectional analysis of 360 paired serum creatinine and cystatin C measurements. Participants whose eGFRcys substantially (>10%) exceeded eGFRcr were identified, and factors associated with this outcome identified in logistic regression analysis. Results The median age was 52 years, 56% were female, and 82% born in Africa or the Caribbean. The eGFRcys substantially exceeded eGFRcr in 42% of participants in the overall cohort, and in 68% of those with eGFRcr 45-75 mL/min/1.73m2. In multivariable analysis, a higher eGFRcr was associated with lower odds (0.59 [0.50, 0.68] per 10 mL/min/1.73m2 increase) of eGFRcys substantially exceeding eGFRcr; a higher BMI was also associated with this outcome while ART regimens inhibiting tubular secretion of creatinine were not predictive. Of the 22 participants with eGFRcr 45-60 mL/min/1.73m2, 16 (73%) had eGFRcys >60 mL/min/1.73m2. Conclusion: We report substantially higher eGFRcys than eGFRcr in a subset of people of African ancestry with suppressed HIV, particularly among those with eGFRcr 45-75 mL/min/1.73m2. In this population, eGFRcys provides clinically useful information irrespective of ART regimen.