Phosphorus (P) unavailability in agricultural soils is a primary cause of the poor development and yield of field crops in arid and semiarid regions. The primary goal of this research project was to investigate the influence of integrated management of beneficial microbes or biofertilizers (BF), organic P-fertilizers, and inorganic P-fertilizers on wheat productivity in a wheat–maize cropping system. Field experiments were carried out during the two consecutive seasons of 2020/2021 (Y1) and 2021/2022 (Y2) according to the two-factorial randomized complete block design with three replications. Factor one consisted of twenty-one treatments of organic and inorganic P-fertilizer combinations, while factor two consisted of two different BF (PSB and Bioaab). One overall control where no P or BF was applied was also included in each replication for comparison. The experiment consisted of six treatments of sole P sources (sheep manure (SM), cattle manure (CM), legume residues (LR), non-legume residues (NLR), single super phosphate (SSP) and rock phosphate (RP)), each applied at a rate of 90 kg P ha−1. Different combinations of organic and inorganic P sources (giving 15 treatments) were applied at a rate of 50% P from each source (i.e., 45 kg P ha−1 applied from different sources in combination). The results revealed that the combined application of SSP+SM produced a significantly higher number of grains spike−1 (23.9%), spikes m−2 (4.5%), and grain yield (40.9%) over the control. Application of PSB produced the maximum number of grains spike−1 (23.9%), spikes m−2 (4.5%), thousand-grain weight (8.3%), grain yield (40.9%), and biological yield (17%) in the wheat crop as compared to Bioaab. It was concluded from the two-year study that integrated use of organic P-fertilizers (animal manures) plus inorganic P-fertilizer (SSP) along with PSB ranked first in terms of higher wheat productivity in a wheat–maize cropping system.