Although interesting studies on N2-fixing legumes have demonstrated the contribution of acid phosphatases (APase) in their phosphorus use efficiency, it is still poorly understood how these enzymes are affected and distributed in bean nodules under P-deficiency. In this study, nodules of six Recombinant Inbred Lines of common bean; RILs 115, 104 and 34 (P-tolerant) and 147, 83 and 29 (P-sensitive) were induced by Rhizobium tropici CIAT899 under hydroaeroponic culture with sufficient (250 μmol P plant−1 week−1) versus deficient (75 μmol P plant−1 week−1) P supply. Phytase and Fructose 1-6 bi-phosphate phosphatase (FBPase) activities were assayed within nodules in which O2 permeability was measured. Our results showed that plant growth, nodulation and symbiotic nitrogen fixation were significantly affected by P- deficiency for all RILs, but this adverse effect was more pronounced in the RILs 147 and 83. For all RILs, the enzymes activities were significantly increased by P- deficiency, but the RILs 115, 104 and 34 maintained higher values as compared to the RILs 147, 83 and 29. Differential tissues-specific expression of phytase transcripts within nodules was detected particularly in infected zone and cortical cells. Additionally, the increased of phytase (35%) and FBPase (49%) enzyme activities under P-deficiency was associated to an increase in efficiency of the rhizobial symbiosis that was positively correlated to an increase in nodule O2 permeability. In conclusion, the variations of APase and phytase activities in nodules depend on genotype and can greatly influence the internal utilization of P, which might result in low P soil tolerance in N2-fixing legumes.