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Background and aims Root residues are an important factor influencing soil phosphorus (P) availability for crop uptake, but how the residues from different species combinations in sole cropping or intercropping systems affect soil P pools remains unclear. Methods Maize and faba bean were planted as either sole crops or intercrops in a P-deficient calcareous soil with and without addition of corresponding previous crop (pre-crop) roots. This was repeated in three cultivations cycles in a greenhouse experiment. Plants sampled in each experiment were analyzed for biomass and P content, and soils sampled from all treatments in the last cultivation were analyzed for soil characteristics. Results Addition of a mixture of intercrop root residues increased biomass, total P content, microbial biomass P concentration and soil acid phosphatase activity, compared with addition of root residues of a single crop. The Hedley soil P fractions from three continuous cultivation cycles differed, depending on root residue source. The sole maize root residue with high C/P ratio caused a considerable depletion of inorganic P (NaHCO3-Pi, NaOH-Pi and 1 M HCl-Pi), and the sole faba bean root residue with lower C/P ratio caused a large depletion in Resin-P and NaHCO3-Po fractions, and the root residue of intercrops with a medium C/P ratio depleted more of the NaHCO3-Po and conc. HCl-Po fractions. However, without root residues, sole faba bean depleted more of the Resin-P, NaHCO3-Pi, NaOH-Pi and NaHCO3-Po fractions than the other two cropping systems did because of its higher P content. Conclusions Adding root residues of mixed species accelerated soil organic P mineralization (NaHCO3-Po and conc. HCl-Po) by increasing microbial biomass P concentrations and acid phosphatase activities, and thus enhanced the intercropping advantage in terms of biomass and P content in a P-deficient soil.