The 2030 Immunization Agenda (IA2030) emphasizes the principle of leaving no one behind, targeting missed children and missed communities as a primary goal in the routine immunization catch-up programming in various countries, particularly in the African region where coverage is suboptimal. Within this cascade of missed children exists children who are zero-dose and under-immunized. In most cases, these outcomes are analysed separately, and yet commonalities exist. Efforts to reduce zero-dose and under-immunized children target women attending the antenatal care (ANC), with health education campaigns and other prenatal interventions. In this study, we propose a model that jointly analyses the two indicators of missed immunization (zero-dose and under-immunization), with attendance of ANC as an endogenous predictor, applying a trivariate copula to account for dependence between the two outcomes and endogenous predictor. We exemplify this using Demographic and Health Survey (DHS) data drawn from Angola and Ethiopia. Our findings show that both zero-dose and under-immunized children were associated with child’s birth order, maternal factors (maternal age and education), and household factors (place of residence and wealth index). Regions that were likely to have zero-dose were equally likely to exhibit high probability of optimal ANC visit, and being under-immunized was highly correlated with vaccine optimal ANC visit in both countries. Overall coverage was suboptimal and displayed huge equity gaps with well-established sub-national inequalities. These findings suggest the need for targeted interventions to reach every community particularly in rural and remote regions, with communications aimed at young mothers, and women with no education, and poorer households. Special reaching-out campaigns should place emphasis in rural areas or socio-economically disadvantaged areas of the communities.