In tropical agro-ecosystem, crop production is constrained by the reduced availability of soil phosphorus (P) due to strong P fixation. A field experiment was conducted for five cropping seasons on an alkaline Fluvisol to assess the integrated effect of six system-based fertilizer P rate (kg P2O5 ha−1) in maize (M)–chickpea (C) rotation [M0–C0, M0–C40, M30–C0, M30–C40, M60–C0, M60–C40], two manure treatments [no farmyard manure (FYM), FYM at 5 t ha−1], and two phosphate solubilizing bacteria (PSB) treatments [no PSB, PSB seed treatment in chickpea] on soil available-P, soil–plant P dynamics, balance, P use efficiency, and system productivity. Combined application of fertilizer P and FYM had a strong positive impact on soil available-P, soil biochemical properties, P acquisition and crop productivity. Conversely, the effect of PSB was marginal. Treatment M60–C40 + FYM + PSB increased soil available-P by 56% at the end of 5-year rotation; where 53% depletion was noticed in treatment M0–C0 − FYM − PSB (control). Treatments M30–C40 + FYM ± PSB, M60–C0 + FYM ± PSB, and M60–C40 + FYM ± PSB had a positive trend of soil available-P. The order of fertilizer P treatments for P uptake and annual P balance was M60–C40 > M30–C40 > M60–C0 > M0–C40 > M30–C0 > M0–C0. FYM application improved P recovery efficiency by 71%. Soil microbial biomass carbon, dehydrogenase and alkaline phosphatase, and soil pH had significant relationship with available-P (p < 0.01). Notably, treatments M30–C0 + FYM + PSB and M60–C40 − FYM − PSB had a similar effect on maize productivity (4.1–4.2 t ha−1). Likewise, treatments M60–C0 + FYM + PSB and M60–C40 − FYM − PSB were comparable for chickpea productivity (p > 0.05). Therefore, integration of manure and fertilizer P is recommended for increasing the productivity and P use efficiency in maize–chickpea rotation in tropical alkaline soil.