In May 2018, the non-governmental organization (NGO) Doctors with Africa CUAMM began to implement an intervention to strengthen Chiulo Hospital’s public health section to deliver immunization services in Mucope Comuna, Ombadja District. We aimed to evaluate the effect of this intervention. During the intervention period, actions such as staff training, improvement in the monitoring of vaccine stockpile, and the involvement of Community Health Workers were performed. The effects of the intervention on the number of vaccine doses administered were examined using negative binomial regression. Doses administered were 14,221 during the intervention period and 11,276 in the pre-intervention one. The number of administered doses was 26% higher (95% CI 9%–45%) in the intervention period than in the pre-intervention period. This was driven by vaccine doses administered during outreach sessions, where a statistically significant increase of 62% (95% CI 28%–107%) was observed. Regarding individual vaccines, statistically significant increases in the number of doses were observed for OPV2 (76%), OPV3 (100%), Penta3 (53%), PCV3 (53%), and Rota2 (43%). The NGO interventions led to improved delivery of immunization services in the study area. Greater increases were observed for vaccine doses that are more likely to be missed by children.