This study aims to determine the quality control indices and proper storage conditions for Ethiopian Yirgacheffe (EY) coffee. An instrumental analysis by SPME-GC-MS and a consumer sensory evaluation using a CATA questionnaire with a 9-point hedonic scale were conducted. The most abundant eleven aroma compounds of EY coffee were identified through SPME-GC-MS analysis. Among the three variables examined—coffee form (beans vs. powder), storage temperature, and storage duration—storage temperature (p < 0.0001) was identified as the most influential factor affecting the sensory quality of EY coffee products. Interaction statistical analysis of instrumental and sensory data identified 2,4-bis(1,1-dimethylethyl)-phenol as the key compound negatively affecting EY coffee's aroma, while N-furfuryl pyrrole was the most positive contributor to flavor quality. These findings were strongly supported by Pearson correlation coefficients and partial least squares (PLS) regression analysis (r = 0.75). Monitoring the levels of compounds like N-furfuryl pyrrole and 2,4-bis(1,1-dimethylethyl)-phenol can help predict the aroma profile of EY coffee products, supporting quality control during processing and storage. Although the mechanisms behind the formation and degradation of these compounds are still under investigation, understanding their variations can guide better storage practices. Avoiding improper storage temperatures is recommended to maintain optimal quality, as this helps preserve flavor and extend shelf life.