The primary goal of integrated nutrient management (INM) strategies is to substitute a portion of chemical fertilizers with a more sustainable and environmentally safe organic compost in order to mitigate soil degradation, improve crop production, and protect the environment. Therefore, the present study was conducted to assess the impacts of different INM practices, namely full-dose NPK (T1), compost of cow manure at 5 t ha−1 (T2), compost of poultry manure at 5 t ha−1 (T3), compost of mixed sheep and camel manure at 5 t ha−1 (T4), 50% NPK combined with the mixture of the three types of composts at the rate of 5 t ha−1 (T5) or 10 t ha−1 (T6), and mixture of the three types of composts at the rate of 10 t ha−1 (T7), 15 t ha−1 (T8), or 20 t ha−1 (T9) with or without biofertilizers for each treatment on several physiochemical and biological proprieties of soil and final grain yield of field crops after 2 years of field-scale experiments. The results showed that all INM practices generally significantly (p < 0.05) improved the initial values of all tested soil physiochemical and biological proprieties, whereas improvement was more prominent for the plots treated with T5–T9, compared with those treated with T1–T4. Seed inoculation with biofertilizers also significantly (p < 0.05) increased different soil proprieties by 2.8–12.0%, compared to that of the non-inoculation treatment. Principal component analysis revealed that most soil chemical properties were closely associated with T5–T6 treatments, while most soil physical and biological properties appeared to be more related to T7–T9 treatments. Our results indicated that recycling agricultural wastes into new productive composts and integrating it into appropriate INM practices as shown in T5–T9 treatments may induce favorable changes in soil properties and improve crop production under arid conditions even in the short term.