Fertilizers based on phosphate–metal–humate complexes are a new family of compounds that represents a more sustainable and bioavailable phosphorus source. The characterization of this type of complex by using solid 31P NMR in several fertilizers, based on single superphosphate (SSP) and triple superphosphate (TSP) matrices, yielded surprising and unexpected trends in the intensity and fine structure of the 31P NMR peaks. Computational chemistry methods allowed the characterization of phosphate–calcium–humate complexes in both SSP and TSP matrices, but also predicted the formation of a stable sulfate–calcium–humate complex in the SSP fertilizers, which has not been described previously. The stability of this complex has been confirmed by using ultrafiltration techniques. Preference towards the humic substance for the sulfate–metal phase in SSP allowed the explanation of the opposing trends that were observed in the experimental 31P NMR spectra of SSP and TSP samples. Additionally, computational chemistry has provided an assignment of the 31P NMR signals to different phosphate ligands as well as valuable information about the relative strength of the phosphate–calcium interactions within the crystals.