Matrix bound phosphine (MBP) in sediment is a widely existing yet often overlooked biologically available phosphorus pool in lakes. We firstly investigated the composition, spatial distribution, and potential environmental risks of MBP in the deep oligotrophic Fuxian Lake and shallow eutrophic Xingyun Lake using a pre-column cold trap enrichment-gas chromatography method. Results showed that the free gaseous phosphine (FGP) concentrations Fuxian Lake and Xingyun Lake were 5.39 ± 1.43 μg P/L and 8.81 ± 2.81 μg P/L, respectively, which accounted for approximately 31.87% to 73.75% of the soluble reactive phosphorus (SRP) in the overlying water, indicating that PH3 was an important component of the P cycle in both lakes. The total MBP (TMBP), porewater-soluble MBP (PMBP), and labile bound MBP (LMPB) in the sediments of Fuxian Lake and Xingyun Lake were 3.59 ± 0.89 ng/kg, 0.98 ± 0.24 ng/kg, and 0.68 ± 0.24 ng/kg; 122.84 ± 26.90 ng/kg, 0.83 ± 0.20 ng/kg, and 0.60 ± 0.18 ng/kg, respectively. TMBP concentrations in Xingyun Lake were found to be significantly higher than those in Fuxian Lake, with pronounced spatial heterogeneity in MBP distribution observed in both lakes. This heterogeneity was characterised by elevated concentrations in the northern regions compared to the southern and central areas, which served as primary inflow areas. The northern Fuxian Lake maintained persistent strongly anaerobic conditions which favored MBP generation. In contrast, the northern Xingyun Lake received substantial inputs of agricultural and domestic wastewater, providing important precusor substance for MBP production. These findings offered scientific insights into the biogeochemical P cycle in plateau lakes.