A new effective one-stage method for production of molten defluorinated phosphates in the submerged combustion melter (SCM) for feed and fertilization in agriculture was developed and tested. The method involves melting raw phosphate ores (phosphate rock, apatite, etc.) in a SCM with certain additives (phosphoric acid, sand, etc.) with consecutive melt draining and granulation. Specific to the melting process is the use of a gas−air mixture with direct combustion inside a melt. Located inside the melt are high-temperature zones with increased reactivity of the gas phase, the existence of a developed interface surface, and intensive mixing, leading to intensification of the defluorination process. The high specific heat of the molten materials and their intensive mixing help the fast melting of coarse-grade and even-lump-size material loaded in the melt. The ability to use granulated charge allows effective reprocessing of the raw phosphate materials and a significant decrease in dust entrainment compared with rotating kilns and cyclone furnaces. The experimental data for different aspects of the proposed method are presented. The viscosities of the melts and their impact on the melting temperature are also discussed. The granulated molten defluorinated phosphate can be used as an effective fertilizer and for feed in agriculture.