Although 91% of 12–23-month-old children in Indonesia received at least one immunization in 2013, only 76% completed DTP3 immunization. This percentage is below the UNICEF and WHO recommended standards. Thus, this study aims to investigate trends, spatial disparities, and social determinants related to low coverage of DTP3 immunization in Indonesia. Using a multilevel approach, we analyzed data from 305,090 12–23-month-old children living across approximately 500 districts in Indonesia to study demand and supply factors determining DTP3 immunization status. We examined unique, nationally representative data from the National Socioeconomic Survey (Survei Sosial Ekonomi Nasional or Susenas) and Village Potential Census (Potensi Desa or Podes) from 2004 to 2016. The percentage of children receiving complete DTP3 immunization increased from 37.8% in 2004 to 75.9% in 2016. Primarily income, parity status, and education, showed influence on DTP3 coverage. Among individual-level factors, the presence of a professional birth attendant was the most influential factor. At the district level, the factors varied. Low progress in DTP3 immunization status in Indonesia is due to huge disparities across the country’s islands, in the density of health services, and in household socioeconomic status.