Universal health coverage is a national priority in Mexico, with active efforts to expand public healthcare system access, increase financial protection and improve quality of care. We estimated effective coverage of multiple conditions within the Mexican Institute of Social Security (IMSS), which covers 62 million individuals. We identified routinely collected performance indicators at IMSS from 2016 related to use and quality of care for conditions avertable with high-quality healthcare; where candidate indicators were available, we quantified need for service from a population-representative survey and calculated effective coverage as proportion of individuals in need who experience potential health gains. We assessed subnational inequality across 32 states, and we weighted conditions by relative contribution to national disease burden to estimate composite effective coverage. Conditions accounting for 51% of healthcare-avertable disability-adjusted life years lost in Mexico could be assessed: antenatal care, delivery care, newborn care, childhood diarrhoea, cardiovascular disease and diabetes. Estimated effective coverage ranged from a low of 27% for childhood diarrhoea to a high of 74% for newborn care. Substantial inequality in effective coverage existed between states, particularly for maternal and child conditions. Overall effective coverage of these six conditions in IMSS was 49% in 2016. Gaps in use and quality of care must be addressed to ensure good health for all in Mexico. Despite extensive monitoring of health status and services in Mexico, currently available data are inadequate to the task of fully and routinely assessing health system effective coverage. Leaders at IMSS and similar healthcare institutions must be more purposeful in planning the assessment of population need, utilization of care and quality impacts of care to enable linkage of these data and disaggregation by location or population sub-group. Only then can complex health systems be fairly and fully evaluated.