Chocolate storage is critical to the quality of the final product. Inadequate storage, especially with temperature fluctuations, may lead to a change in crystal structure, which may eventually cause fat bloom. Bloom is the main cause of quality loss in the chocolate industry. The impact of various storage conditions on the flavor quality of dark chocolate was determined. Dark chocolate was stored in different conditions leading to either fat or sugar bloom and analyzed at 0, 4, and 8 weeks of storage. Changes in chocolate flavor were determined by volatile analysis and descriptive sensory evaluation. Results were analyzed by analysis of variance (ANOVA), cluster analysis, principal component analysis (PCA), and linear partial least-squares regression analysis (PLS). Volatile concentration and loss were significantly affected by storage conditions. Chocolates stored at high temperature were the most visually and texturally compromised, but volatile concentrations were affected the least, whereas samples stored at ambient, frozen, and high relative humidity conditions had significant volatile loss during storage. It was determined that high-temperature storage caused a change in crystal state due to the polymorphic shift to form VI, leading to an increase in sample hardness. Decreased solid fat content (SFC) during high-temperature storage increased instrumentally determined volatile retention, although no difference was detected in chocolate flavor during sensory analysis, possibly due to instrumental and sensory sampling techniques. When all instrumental and sensory data had been taken into account, the storage condition that had the least impact on texture, surface roughness, grain size, lipid polymorphism, fat bloom formation, volatile concentrations, and sensory attributes was storage at constant temperature and 75% relative humidity.