Freeze-drying is one of the most expensive and most energy intensive processes applied in food technology. Therefore, there have been significant efforts to reduce the freeze-drying time and decrease its energy consumption. The aim of this work was to analyze the effect of pulsed electric field (PEF), ultrasound (US), and hybrid treatment (PEF-US) and compare them with the effect of blanching (BL) on the freeze-drying kinetics, energy consumption, greenhouse gasses emission, and physical quality of the product. The freeze-drying process was applied to red bell peppers after pretreatment operations. Results showed that application of BL, PEF, US, or PEF-US reduces freeze-drying time and decreases energy consumption. Among the tested methods, the combination of PEF performed at 1 kJ/kg and US was the most effective in reduction of greenhouse gas emission. BL samples exhibited the highest porosity, but from a statistical point of view, most of the PEF-US treated materials did not differ from it. The smallest color changes were noted for US pre-treated bell peppers (ΔE = 9.4), whereas BL, PEF, and PEF-US material was characterized by ΔE of 15.2–28.5. Performed research indicates the application of pre-treatment may improve the sustainability of freeze-drying process and quality of freeze-dried bell pepper.