The importance of inorganic fertilizers in squash crop productivity is enormous. However, the continuous use of inorganic fertilizers constitutes a serious problem to the environment and human health due to nitrate accumulation. Thus, two seasons (2020 and 2021) of field trials were carried out to investigate the effects of bio-organic amendments on squash under arid land conditions in Saudi Arabia. The bio-organic amendments were comprised of humic acid (HA) at three levels (0, 50 and 100 L/ha), inoculation of a cellulose-decomposing bacterium (CDB; Geobacillus stearothermophilus SSK-2018) and wheat straw at four levels (0, 20 and 30 t/ha and NPK 20:20:20 at 600 kg/ha as a positive control). A randomized split-split plot design replicated three times was used in laying out the field trials. The independent application of HA, CDB and wheat straw significantly (p ≤ 0.05) improved squash growth, yield and water-use efficiency in both seasons. Furthermore, HA significantly (p ≤ 0.05) reduced fruits’ nitrate content. HA (100 L/ha) reduced nitrate content in squash fruits by 87% and 71.6% compared to the control in 2020 and 2021, respectively. The application of 20 t/ha of wheat straw significantly (p ≤ 0.05) reduced nitrate accumulation in fruits compared to the positive control (NPK) by 5.9% and 13.6% in 2019/20 and 2020/21, respectively. Regression analysis shows that increased nitrate accumulation in fruits results in decreased squash growth and fruit yield. This study demonstrates the significance of bio-organic amendments in improving squash growth and yield while reducing nitrate accumulation in fruits.