The objective of this study was to evaluate the individual and synergic effects of the application of Biochar (B), Humic Substances (HS), and Gypsum (G) on the soil properties of a saline–sodic soil, and plant growth and seed quality (polyphenols, protein and yield) of quinoa. Treatments included (B) 22 t ha⁻¹, (HS) 5 kg ha⁻¹, and (G) 47.7 t ha⁻¹. Two quinoa genotypes from Arid Zones (AZ-51 and AZ-103) were selected and established in eight treatments. The B + HS + G combined treatment resulted in increases in root biomass of 206% and 176% in AZ-51 and AZ-103, respectively. Furthermore, electrical conductivity (ECe), sodium adsorption ratio (SAR), and exchangeable sodium percentage (ESP) decreased significantly in all treated soils. When compared to the control, ESP decreased 11-fold in the G treatment, and 9–13-fold in the B + G; B + HS; and B + HS + G treatments. Similarly, soil microbial biomass increased 112% and 322% in the B + HS + G treatment in AZ-51 and AZ-103 genotypes, respectively. Therefore, it can be concluded that the application of combined amendments (B + HS + G) represents an alternative for reclaiming degraded soils, including saline–sodic soils.