We developed the first time series of carbon stocks (Aboveground- AGB, Belowground- BGB and Soil Carbon Stocks-SCS) for Western Bahia from 1990-2018. This region is located at the largest and most dynamic agricultural frontier in Brazil known as MATOPIBA.The methods used here to develop carbon stocks time series combine data from the literature for Aboveground (AGB) and Belowground (BGB), and Soil Carbon Stocks measurements (SCS) for six land use and land cover classes (irrigated agriculture, rainfed agriculture, pasture, Savana Formations, Grasslands formations, and Forest formations) with modeling and remote sensing techniques. All maps have a scale of 1:15,000 (30 m spatial resolution) and are in NetCDF (network Common Data Form) format.These time series were generated and discussed in the study "Carbon stocks and dynamics of different land uses on the Cerrado agricultural frontier", published in PLOS ONE journal. Data sources, assumptions and calculations are described in detail in the reference above.