Reuse poultry manure (PM) and vinasse (V) is a promising technology for the sustainability of various agricultural systems without environmental impact, but its effects on soil fertility index (SFI), hydraulic conductivity (Ks), porosity (TP), available water (AW), and spinach (Spinacia oleracea L.) growth in calcareous soils are poorly understood. Therefore, we studied the residual effect of combining PM either individually or mixed with V at different rates in pots. This study found that adding PM alone or in conjunction with V at various application rates resulted in an important improvement in SFI, Ks, TP, AW, and spinach yield. Vinasse contributed to an increase in more than 20% of the organic matter when adding it as 4.2 g V and 6.3 g PM kg−1 soil, and gave the best results in the organic matter fresh weight of spinach plant, SFI, and AW by 43.8%, 26.33%, 41.24%, and 63.63% compared to control. Spinach leaf uptake of NPK rose considerably when the soil was treated with PM alone or in combination with V. The SFI, cation exchange capacity (CEC), available N (AN), available P (AP), Ks, and AW were shown to be positively associated with spinach fresh weight utilizing principal component analysis, but soil electrical conductivity (EC), exchange sodium percentage (ESP), pH, and bulk density (BD) were found to be negatively correlated. Additionally, it was estimated by the K-Nearest Neighbors technique that under certain soil conditions, including AP 14.89 mg kg−1, AN 38.25 mg kg−1, microbial biomass carbon (MBC) 2.47 mg kg−1, CEC 11.66 cmol kg−1, exchangeable sodium percentage (ESP) 11.65%, and SFI 26.55%, spinach fresh weight increases to 13.8 t ha−1. These findings show how adding PM and V can improve soil quality and enhance nutrient uptake, all of which can contribute to a higher productivity of spinach and sustainability in calcareous soils.