Due to high cost of P fertilizers, natural rock phosphate (RP) is considered a good alternative for P fertilizer. Phosphorus biofertilizers in the form of microorganisms enhance RP solubalization and increase its availability to the plant. An experiment was conducted to determine yield, yield components, phosphorus and nitrogen uptake of wheat crop as influenced by different methods of effective microbes application with composts at research farm of The University of Agriculture Peshawar, during rabi season 2013 – 2014. There were eleven treatments control, N and K as basal dose, organic waste compost (C-I), C-I + effective microbes soil application (EM-I), C-I + effective microbes foliar application (EM – II), C-I + Half EM–I + Half EM-II, Farm yard manure (C-II), C-II + EM-I, C-II + EM – II, C-II + Half EM–I + Half EM-II. Maximum grain yield of 5590 kg ha-1, total dry matter yield of 13092 kg ha-1, thousand grain weight of 51.17 g, soil N content of 3680 mg kg-1, P content of 5.925 mg kg-1 were observed in the treatment of FYM compost with soil application of EM, which were statisticaly at par with SSP treatment. Plant N and P uptakes were significanly improved by the treatment of FYM compost with soil application of EM followed by SSP treatment. The constantly better performance of FYM compost with soil application of EM regarding wheat yield, yield components, N and P uptake suggested that it may be used as an alternative source of P fertilizer.