As bell peppers are produced year-round via greenhouse-based technology, the fruit quality of bell peppers fluctuates greatly depending on the bell pepper cultivar during winter. Thus, this study aimed to evaluate the seasonal fluctuation effects on fruit quality attributes, mineral nutrients, and targeted major metabolites in the 'Scirocco', 'DSP7054', and 'Volante' bell pepper cultivars grown in greenhouse cultivation system from September to June. Overall, fruit physiological and biochemical performance clearly diverged depending not only on bell pepper cultivar, but also on harvest time. The results of the partial least square-discriminant analysis (PLS-DA) loading plot indicated that amino acids were closely associated with fatty acids, however less associated with most mineral nutrients, chlorophylls, and physiological fruit quality attributes. According to the results of the variable importance in projection (VIP) score plot, 12 variables were highly important during winter season, regardless of bell pepper cultivars. While pericarp colour variables differentially responded to the pericarp colour of bell pepper cultivars, fruit quality attributes, soluble carbohydrates, citric acid, malic acid, glutamine, K, Mg, and total antioxidant scavenging activities were highly variable depending on bell pepper cultivar and sampling time during the winter season. The results of the correlation coefficient networks indicated that the overall fruit performance based on the results of physiological fruit quality attributes, mineral nutrients, and targeted major metabolites was highly different depending on the bell pepper cultivar. Thus, the overall pattern of correlation coefficient network was much more distinctive in 'Volante' cultivar than in 'Scirocco' and 'DSP7054' cultivars during the winter season. Therefore, the results indicate that fruit quality and performance derived from mineral nutrients and targeted major metabolites fluctuated depending on the bell pepper cultivar during the winter season.