The relevance of involving substandard raw materials for the production of composite phosphorus-containing fertilizer production is significant due to the problem of providing food products for the growing population of the Earth. The main raw materials for phosphorus and composite phosphorus-containing fertilizer production are natural phosphate ores—phosphorites. However, in the process of mining and crushing, ~55–60% phosphorite ore fines are formed—a fraction of less than 10 mm, which is unsuitable for traditional processing into composite phosphorus-containing fertilizers. This article presents the results of physicochemical studies of the substandard fine fraction of phosphorite ore and the results of the studies of the possibility of their direct processing into phosphorus and composition of phosphorus-containing fertilizers using methods of mechanical and mechanochemical activation in the “Activator 4” planetary mill. The findings of the studies performed confirm the rather high efficiency of phosphorite ore fines’ mechanical activation and phosphorite-containing mixtures’ mechanochemical activation, which make it possible to significantly increase the content of assimilable phosphorus pentoxide P2O5 in composite phosphorus-containing fertilizers. The proposed innovative technology has fundamental differences from existing technologies, since the mechanochemical activation of a mixture of phosphorite ore fines and functional components will allow for direct acid-free and waste-free processing into phosphorus and composite phosphorus-containing mineral fertilizers.