Standardized and repeatable techniques for microfermentation and drying small samples (<100 g) of cacao (Theobroma cacao), also known as cocoa, are necessary to identify new varieties having high yield and quality. Sensory analyses of the processed cacao seed (bean) are a critical component to develop varieties for Hawaii’s cacao to chocolate industry. A microfermentation and drying system capable of processing multiple samples of mucilage-covered cacao beans ranging from 60 to 6000 g was developed. The effects of fermentation variables, genetic background, management, site, and season on quantitative and qualitative attributes can be studied using this protocol. Beans processed using the College of Tropical Agriculture and Human Resources (CTAHR) bag system (CBS) are inoculated with microorganisms on their fruit (pod) surface. This enables a better assessment of the terroir of sites when the dried fermented beans are roasted and processed. Clean, inexpensive, disposable polyethylene bags serve as fermentation vessels. The fermentery has a temperature controller that follows a fermentation temperature profile. Sun drying is replaced by drying in the laboratory. Two-month storage in ambient outdoor humidity and temperature completes the protocol. The CBS is an improvement to existing cacao microfermentation methods because beans from single pods can be fermented. No microbial isolates, inoculums, or foreign pulp from other trees and sites are used. Less labor is required to maintain the fermentation. In laboratory drying is less variable than sun drying. The CBS is a flexible and reliable method to microferment cacao for scientists, small growers, and hobbyists.