Subnational Population Estimates (SPE) in Latin America are useful to implement new public policies in subnational areas with internal armed conflicts or difficult to access. In this work, we propose to combine a Population Base Statistical Register (PBSR) and the Official Population Projections (OPP) using a Bayesian approach to produce SPE. Our proposed procedures are useful for computing SPE of the population size or the SPE of the population size in percentage SPE (%). However, we focused on SPE (%) due to some data restrictions and to ensure data confidentiality. In this article, the PBSR is constructed using multiple administrative sources with registers from the health, education, vital statistics systems, tax registration, and, more importantly, the registers of the victims of the current internal armed conflict in Colombia. We also propose new fast Markov chain Monte Carlo algorithms to produce SPE (%) using data augmentation procedures to address the complications caused by the resulting joint posterior containing gamma functions. We implement our proposal to compute SPE (%) by age and sex groups in the municipality of Jamundí in Colombia which is currently affected by poverty, forced displacement, and the internal armed conflict and evaluate the accuracy with a Population Census.