Phosphorus deficiencies are limiting crop production in agricultural soils worldwide. Locally available sources of raw phosphate rock (PR) are being recognized for their potential role in soil fertility improvement. Phosphorus bioavailability is essential for the efficiency of PRs and can be increased by acid treatments. The utilization of organic acid producing micro-organisms, notably Aspergillus niger, presents a sustainable alternative to the use of strong inorganic acids, but acid production of A. niger strongly depends on the mineral content of the growth media. This study compared the phosphorus mobilization efficiency of two biological treatments, namely addition of acidic cell-free supernatants from A. niger cultivations to PRs and the direct cultivation of A. niger with PRs. The results show that addition of PR to cultivations leads to significant differences in the profile of organic acids produced by A. niger. Additions of PR, especially igneous rocks containing high amounts of iron and manganese, lead to reduced citric acid concentrations. In spite of these differences, phosphorus mobilization was similar between treatments, suggesting that the simpler direct cultivation method was not inferior. In addition to citric acid, it is suggested that oxalic acid contributes to PR solubilization in direct cultivations with A. niger, which would benefit farmers in developing countries where conventional fertilizers are not adequately accessible.