This study aimed to evaluate the interaction between filter cake (FC), and phosphorus fertilizers with differing solubility on the growth and P nutrition of sugarcane. Effects of soil amendment with FC on different soil P fractions and influence on microbial community structure in the rhizosphere were also assessed. Two glasshouse experiments were conducted with completely randomized block designs. The first experiment evaluated rates of FC using a factorial design (5 × 2): 0, 2.5, 5, 10 and 15 g FC kg−1 soil applied as either broadcast in bulk soil or in the planting furrow. The second experiment used a factorial design (2 × 3): without and with FC (5 g kg−1 soil, dry basis), both without P (NP) and with P supplied as either triple superphosphate (TSP) or as rock phosphate (RP), both at the rate of 78.4 mg kg−1 based on total P. Microbial community structure was determined using TRFLP and dynamics of soil P by Hedley fractionation. Filter cake applied at increasing rates in the absence of P was effective in increasing shoot growth and P uptake by plant, particularly when applied to bulk soil as compared to furrow application. Also, FC improved P uptake and increased the availability of labile inorganic P in the rhizosphere and modified the structure of fungal and bacterial communities, whereas only bacterial and archaea communities were influenced by P fertilizer use. Filter cake was more effective when combined with RP, with increased growth and P utilization and thus can be considered as a feasible and practical option for farmer use in substitution to TSP, a more expensive source.