Since the discovery of (L)-phosphinothricin in the year 1970, the development of α-amino acids bearing a phosphorus group has been of renewed interest due to their diverse applications, including their use in [¹⁸F]-fluorolabeling, as fluorescent probes, as protecting groups and in the reversible immobilization of amino acids or peptide derivatives on carbon nanomaterials. Considerable progress has also been achieved in the field of antiviral agents, through the development of phosphoramidate prodrugs, which increase significantly the intracellular delivery of nucleoside monophosphate and monophosphonate analogues. This review aims to summarize the strategies reported in the literature for the synthesis of P(III), P(IV) and P(V) phosphorus-containing amino acids with P–C, P–O, P–S or P–N bonds in the side chains and their related applications, including their use in natural products, ligands for asymmetric catalysis, peptidomimetics, therapeutic agents, chemical reagents, markers and nanomaterials. The discussion is organized according to the position of the phosphorus atom linkage to the amino acid side chain, either in an α-, β-, γ- or δ-position or to a hydroxyl, thiol or amino group.