Bell peppers (Capsicum annuum L.) are of great importance and have high productive potential in Brazil, especially in the Northeast region; however, their production is limited due to salinity problems in water and soil. The objective of this study was to evaluate sources and methods of calcium application for mitigating salt stress in bell pepper plants grown in a substrate-based hydroponic system. The experiment was conducted using a split-plot design in a 2 × 2 × 3 layout with four replicates, consisting of two application methods (substrate and spray), two ECiw levels (0.5 and 5.0 dS m⁻¹), and three calcium sources (no calcium—NCa; calcium nitrate—Ca(NO₃)₂; calcium complexed with amino acids—Ca-AA). Forty-two days after transplanting, gas exchange analysis, chlorophyll a, b, and total chlorophyll indices, chlorophyll fluorescence, fruit number and weight, and yield per plant were measured. Ca-AA showed higher photosystem II efficiency when applied via the substrate and higher stomatal conductance (28.10%), resulted in higher fruit yield compared to the other treatments, and contributed to a reduction in apical rot. Meanwhile, the application of Ca(NO₃)₂ improved electron transport in photosystem II by 5.46%, gas exchange, and increased chlorophyll b and total chlorophyll indices by 29.62% and 10.93%, respectively. It is concluded that the application of Ca sources, especially Ca-AA, has the potential to mitigate the effects of salt stress on bell pepper plants in a substrate-based hydroponic system, improving their photosynthetic and productive performance.