Enantiodifferentiation of N-protected ethyl and phenyl α-aminophosphonates with application of commercially available cyclodextrins as chiral solvating agent was studied by means of nuclear magnetic resonance spectroscopy. Four cyclodextrins (α-CD, β-CD, γ-CD and HP-γ-CD) were chosen due to the differences in the size of their inner cavities and substitution of the rim, which in turn might change the affinity of the compounds analyzed to these chiral selectors. The influence of solution pD and host concentration on the enantiodiscrimination efficiency was also studied. As a result, a methodology for the simple and rapid assessment of the enantiomeric composition of various N-benzyloxycarbonyl-α-aminophosphonates has been elaborated upon. 2D Rotating frame nuclear Overhauser and exchange spectrometry experiments and continuous variation methods were applied for establishing the molecular recognition mechanism and structure of the guest–host assemblies.