Zero-dose children remain highly vulnerable to vaccine-preventable diseases and can sustain transmission even in highly vaccinated populations. The WHO Immunization Agenda 2030 has prioritised reaching out to these children. We assessed the spatial distribution of zero-dose children together with the associated risk factors in a provincial capital in the Democratic Republic of Congo. A cross sectional survey was conducted in the city of Kikwit between September 28 and October 14, 2022. Data were collected both at household and health area level. QGIS and SATscan were used to describe and identify hotspots among zero-dose children, and a mixed effect logistic regression model was used to identify risk factors. Overall, 1,863 children aged 12-23 months were enrolled. Kikwit city had a 16.3% zero-dose prevalence, with significant variation between and within health zones. Two hotspots were identified through geospatial analysis, each spanning multiple health areas. Multilevel analysis revealed significant clustering at health area level and found six associated risk factors. These include the absence of home visits by community health workers (aOR = 1.90), living more than a kilometre from a health centre (aOR = 1.95), the mother's lack of tetanus vaccination (aOR = 3.16), and inability to name a vaccine-preventable disease (aOR = 3.20). However, secondary (aOR = 0.56) or tertiary (aOR = 0.21) education of mothers/guardians and belonging to Bunda (aOR = 0.36) or Mbala (aOR = 0.52) ethnicity reduced the risk of zero-dose. We observed a high prevalence of zero-dose children with a heterogeneous spatial distribution of epidemiological importance. Due to sub-zonal diversity, a health zone approach to reduce zero-dose immunization appears very limited. Zero-dose prevalence was related to the community health workers' home visit, to the distance of residence to a health centre and to household-level factors. Geospatial results could help in targeting priority health areas and communities for vaccination.