Novel Zr methyl- and ethyl-N,N-bis(methylphosphonates), with formula ZrF2[(O3PCH2)2NHCH3] and Zr[(HO3PCH2)(O3PCH2)NHC2H5]2, respectively, were prepared in mild solvothermal conditions and their structures were solved ab initio by laboratory X-ray powder diffraction data. Despite the chemical homology between the molecular building blocks, and the similar synthetic conditions, the two compounds showed different stoichiometry and crystal structure. A comparative analysis of these structures and that of homologous longer chain Zr phosphonates, previously reported, revealed the important contribution of the hydrophobic groups in the building of the crystal structure, in a way that can be compared to that observed in the assembly of amphiphilic systems.