The aim of the present study was to investigate the relationship between the uptake of phosphorus (P) from rock phosphate (RP) by plants and the enhancement of the biological properties of the soil by compost amendments. In experiments conducted in Wagner’s pots (200 cm2), the enrichment of Andosols with RP at 0, 100, or 200 mg P kg−1 soil was combined with the addition of one of four types of compost at a rate equivalent to 13.3 mg P kg−1 soil or with no compost treatment, and the amended soils were used to grow African millet (Eleusine coracana Gaertn, cv. Yukijirushi) for 60 days. The composts added to the soil were based on poultry manure (PM), cattle manure (CM), sewage sludge (SS), or P-adjusted sawdust (PSD). In an incubation experiment, RP was added at 0 or 150 mg P kg−1 of soil in combination with each of the four types of compost at the same rate of application as in the pot experiment, or with no compost. The uptake of P from RP (RP-P) by plants was highest with PM, followed by CM and PSD, and then SS; it was four- to five-fold more with compost addition than no compost addition. Microbial biomass P was significantly higher when RP was added with PM or CM. RP-P uptake by plants showed a positive correlation (r = 0.72, P < 0.05) with the microbial biomass P in the soil. In the soil incubation, the population density of phosphate-solubilizing bacteria (PSB) was significantly higher in compost-amended soils than in the absence of compost treatment, and was highest with the addition of PM. The available P in soil showed a positive correlation (r = 0.70, P < 0.05) with the population density of PSB. These results show that the uptake of P from RP by plants is enhanced by amendment with compost, especially PM or CM compost, and is strongly related to the biological properties of the soil, such as the microbial biomass P and the population density of PSB.