Small and medium-scale biorefineries are processing facilities designed to produce a portfolio of value-added products with applications in different productive sectors. The Territory of the Southern Coast (TSC) of Bahia in Brazil has a high potential to provide agricultural and forest biomass for these bioindustries. This study focuses on quantifying the biomass of key agricultural crops in the TSC from 1999 to 2019, utilizing data from the Municipal Agricultural Production (MAP) survey conducted by the Brazilian Institute of Geography and Statistics (IBGE). The biomass is subsequently categorized based on its applications in pharmaceutical and other industries, employing the Classification and Regression Tree (CART) algorithm, specifically using the Gini Index. Thus, our results reveal a noteworthy trend over 20 years through a time series analysis. For example, banana production (1.3 Mt) surpassed cocoa production (1.1 Mt) despite cocoa cultivation covering a vast 5.8 million hectares expanse compared to the smaller banana footprint. Cocoa and cassava are significant contributors, representing 41.95% and 30.51% of the total raw material, collectively constituting 72.46% of the TSC biomass. In addition, coffee biomass has been profiled as a raw material with potential applications across various industries, while bananas are oriented towards supplying pharmaceutical inputs. Forest species also have the potential for use in the pharmaceutical industry. In conclusion, small and medium-scale biorefineries can help increase agricultural and forest biomass use to provide inputs for various industries and guarantee positive social impacts for the population.