This analysis describes specific gaps in the quality of health care in Central Africa and assesses the association between quality of clinical care and mortality at age 2–59 months. Regionally representative facility and household surveys for the Democratic Republic of the Congo, Cameroon and Central African Republic were collected between 2012 and 2016. These data are novel in linking facilities with households in their catchment area. Compliance with diagnostic and danger sign protocols during sick-child visits was observed by trained assessors. We computed facility- and district-level compliance indicators for patients aged 2–59 months and used multivariate multi-level logistic regression models to estimate the association between clinical assessment quality and mortality at age 2–59 months in the catchment areas of the observed facilities. A total of 13 618 live births were analysed and 1818 sick-child visits were directly observed and used to rate 643 facilities. Eight percent of observed visits complied with 80% of basic diagnostic protocols, and 13% of visits fully adhered to select general danger sign protocols. A 10% greater compliance with diagnostic protocols was associated with a 14.1% (adjusted odds ratio (aOR) 95% CI: 0.025–0.244) reduction in the odds of mortality at age 2–59 months; a 10% greater compliance with select general danger sign protocols was associated with a 15.3% (aOR 95% CI: 0.058–0.237) reduction in the same odds. The results of this article suggest that compliance with recommended clinical protocols remains poor in many settings and improvements in mortality at age 2–59 months could be possible if compliance were improved.