The variety of navel orange known as “Cara Cara” trees are greatly affected by soil salinity, which adversely influences yield and quality. Therefore, adopting the use of safe and inexpensive materials is crucial in this case. Herein, bio-stimulants (whey protein hydrolysates, and humic acid), and ascorbic acid could be utilized to promote plant growth in both normal and salt-stress environments. Two field trials were implemented to investigate the response of navel orange trees to whey proteins hydrolyzed (WPH) with pepsin (PEH at a concentration of 1000 mg L−1) and papain (PAH at a concentration of 1000 mg L−1), or ascorbic acid (ASA) at a concentration of 1000 mg L−1, and/or humic acid (HA) (applied to the soil at a concentration of 1000 mg L−1). The changes in fruit yield, fruit quality, physio-biochemical attributes, and antioxidant defense systems under salinity stress (with an electrical conductivity of 5.14 dS m−1) were estimated. All treatments involving HA with WPH or ASA significantly improved various fruit yield and quality traits, physiological and photosynthetic performance attributes as well as enzymatic and non-enzymatic antioxidants, comparing to the check treatment in both seasons. In this context, PEH+HA treatment was the efficient practice for increasing fruit yield per tree by 80.3 and 82.7%, total acidity by 162.3 and 250.0%, vitamin C by 10.7 and 13.6%, total soluble solids by 12.5 and 8.3%, net photosynthetic rate by 82.3 and 80.9%, relative water content by 27.9 and 28.0%, and membrane stability index by 44.2 and 43.0%, while decreasing electrolyte leakage by 56.0 and 57.0%, and malondialdehyde by 57.8 and 58.3% during two seasons, respectively, as compared to check treatment. Also, PEH+HA treatment showed the highest potentiality for ameliorating the defensive mechanism indices elevating catalase by 17.3 and 17.2%, super oxide dismutase by 122.2 and 122.1%, and glutathione by 97.9 and 99.0%, while suppressing hydrogen peroxide by 45.7 and 45.6% and superoxide radical by 47.9 and 49.3%, during the two seasons, respectively, as compared to the check treatment. Furthermore, it should be mentioned that the values of most fruit yield and quality traits, photosynthetic efficiency, physiological performance and ant-oxidative indices obtained with application of PAH+HA and ASA+HA treatments were as similar as those of gained by PEH+HA. Therefore, the outcomes of the current study indicated that using integrated PEH+HA, PAH+HA and ASA+HA treatments are considered helpful practices for growing citrus plants and maintaining yield and quality in saline soil circumstances.