In Brazil and in most low- and middle-income countries (LMICs), information about how prepared the health care system is for the rapid aging of the population is scarce. We investigated the prevalence of disability and areas of life affected by disability among elders of the public primary health care in São Paulo and Manaus, Brazil. We investigated whether people with disability visited a primary care professional more frequently, the individual characteristics associated with disability, and differences by city. We randomly selected participants aged ≥60 years (n = 1375). The main outcome was disability, evaluated with the 12-item World Health Organization Disability Assessment Schedule (WHODAS 2.0). Exposure variables were consultation with a family physician, sociodemographic characteristics, health status, social support, and lifestyle. The prevalence of global disability was higher in Manaus (66.2% vs. 56.4% in São Paulo). In both cities, participation and mobility were the areas of life most affected by disability. The number of consultations with a family physician was not associated with disability. The high prevalence of disability and associated risk factors indicates that public primary health care is not meeting the needs of elders in both cities. It is warning because most elders in LMICs live in more underserved communities compared to Brazil.