During the fermentation of cocoa beans, the yeasts produce volatile organic compounds (VOCs). Through reactions associated with amino acid metabolism, yeasts generate important aroma precursors as acetate esters and fatty acid ethyl esters are essential in developing fruity flavors and aromas in the final product (usually chocolate). In addition, some yeasts may have pectinolytic and antifungal activity, which is desirable in the post-harvest process of cocoa. The main yeast species in cocoa fermentation are Saccharomyces cerevisiae, Pichia kudriavzevii, and Hanseniaspora opuntiae. These produce higher alcohols and acetyl-CoA to make acetate–esters, compounds that produce floral and fruity notes. However, there are still controversies in scientific reports because some mention that there are no significant differences in the sensory characteristics of the final product. Others mention that the fermentation of cocoa by yeast has a significant influence on improving the sensory attributes of the final product. However, using yeasts as starter cultures for cocoa bean fermentation is recommended to homogenize sensory attributes such as notes and flavors in chocolate.

This study aimed to identify and evaluate yeasts and lactic acid bacteria (LAB) isolated from Mexican cocoa mucilage (Theobroma cacao) and coffee pulp (Coffea arabica) for their potential use as sourdough starter co-cultures to improve bread quality. Functional screens included assessments of amylolytic, proteolytic, and phytase activities, CO₂ production, acidification capacity, and exopolysaccharide (EPS) synthesis. Saccharomyces cerevisiae YCTA13 exhibited the highest fermentative performance, surpassing commercial baker’s yeast by 52.24%. Leuconostoc mesenteroides LABCTA3 showed a high acidification capacity and EPS production, while Lactiplantibacillus plantarum 20B3HB had the highest phytase activity. Six yeast–LAB combinations were formulated as mixed starter co-cultures and evaluated in sourdough breadmaking. The B3Y14 co-culture (LABCTA3 + YCTA14) significantly improved the bread volume and height by 35.61% and 17.18%, respectively, compared to the commercial sourdough starter, and reduced crumb firmness by 59.66%. Image analysis of the bread crumb revealed that B3Y14 enhanced the crumb structure, resulting in greater alveolar uniformity and a balanced gas cell geometry. Specifically, B3Y14 showed low alveolar regularity (1.16 ± 0.03) and circularity (0.40 ± 0.01), indicating a fine and homogeneous crumb structure. These findings highlight the synergistic potential of selected allochthonous yeast and LAB strains in optimizing sourdough performance, positively impacting bread texture, structure, and quality.