Development of Fermentation Strategies for Quality Mild Coffee Production (Coffea arabica L.) Based on Oxygen Availability and Processing Time

Fermentation is a crucial stage in the production of washed mild coffees, as it enables the generation of compounds that influence overall quality. The conditions to optimize this process are still unknown. This study evaluated the effects of fermenting coffee fruits and depulped coffee under two conditions: an open tank (semi-anaerobic-SA) and a closed tank (self-induced anaerobic fermentation, SIAF) over 192 h. Samples were taken every 24 h using a sacrificial bioreactor. A randomized complete block design with a factorial arrangement (2 × 2 + 1), plus a standard control, was employed, incorporating two factors: coffee type and fermentation condition. High-throughput sequencing of 16S and ITS amplicons identified an average of 260 ± 71 and 101 ± 24 OTUs, respectively. <i>Weisella</i> was the dominant lactic acid bacteria, followed by <i>Leuconostoc</i> and <i>Lactiplantibacillus</i>. Acetic acid bacteria, mainly <i>Acetobacter</i>, were more abundant under semi-anaerobic conditions. The yeast genera most affected by the fermentation condition were <i>Pichia</i>, <i>Issatchenkia</i>, and <i>Wickerhamomyces</i>. Repeated measures analysis revealed significant differences in pH, glucose consumption, lactic acid production, dry matter content, embryo viability, and the percentage of healthy beans. Principal component analysis was used to develop an index that integrates physical, physiological, and sensory quality variables, thereby clarifying the impact of each treatment. Samples from shorter fermentation times and SIAF conditions scored closest to 1.0, reflecting the most favorable outcomes. Otherwise, samples from longer fermentation times in both depulped and coffee fruits scored 0.497 and 0.369, respectively, on the SA condition. These findings support technically and economically beneficial fermentation strategies.