Agriculture is a critical socioeconomic sector in Egypt, generating approximately 10–15% of the national gross domestic product. Organic agricultural wastes from food industries are not commonly used as soil ameliorants in Egypt. Therefore, several promising ameliorant systems are poorly developed for Egyptian soils reclamation. So, four directions were applied to developing organic wastes to enhance soil–plant productivity: (1) using industrial wastes as soil ameliorants such as brewer’s spent grain (S2). (2) production of vermicompost from spent grain (VC). The 3rd direction was to extract two humic substances from vermicompost and enrich it with microelements (HS, HS-M). The last direction was the inoculation of Azospirillum to soil (Az). The field experiments were carried out in plots sown in November 2020 with wheat plants for 6 months. The results showed that the Az, VC, S2, HS, and HS-M treatments increased soil fertility and plant growth parameters compared to NPK and control. The mean fresh weight for VC and S2 was 17.45 and 15.92 g plant⁻¹compared to control, and NPK was 12.72 and 14.56 g plant⁻¹, respectively. The higher contents of soil micronutrients were observed with VC and HS-M ameliorants, while the lowest was observed with NPK. Applying S2 and Az to the soil contributed to a significant (P ≤ 0.05) increase in Ca²⁺ and Mg²⁺ ions. In conclusion, based on sustainable development goals, this work successfully transferred non-useful organic wastes to environmentally friendly organic wastes to be used as clean soil ameliorants based on sustainability and biological conformity.