Phosphorus and uranium are both vital elements for society. In recent decades, fears have arisen about the future availability of low-cost phosphorus and uranium. This has resulted in pressure to de-centralize production of both elements by utilizing lower-grade or complex deposits. The research presented here focused on phosphorus-containing apatite ores with uranium impurities; in order to separate uranium by selective and sequential bioleaching before phosphorus leaching. This would create an alternative process route for solvent-extraction, used to remove/recover uranium from the phosphorus acid product of apatite H2SO4 wet process. In this work, it was seen that the used fluorapatite ore required 24 h leaching at pH 1 by H2SO4 to result in 100% leaching yield for phosphorus. As this ore did not contain much uranium, an artificial fluorapatite-uranium ore was prepared by mixing standard uranium ore and fluorapatite. The research with this ore showed that 89% of uranium dissolved in 3 days at pH > 2 and leaching was improved by applying Fe3+ oxidant. In these conditions only 4% of phosphorus was leached. By prolonged (28 days) leaching 95% uranium yield was reached. According to the experiments, the iron in the uranium leach solution would be mainly Fe3+, which allows the use of H2O2 for uranium recovery and then direct use of spent leachate for another uranium leaching cycle. After the dissolution of uranium, 90% of phosphorus was dissolved by decreasing the pH to 1.3. This was done by bioleaching, by utilizing biogenic sulfur oxidation to sulfuric acid.