Allophanes are poorly crystalline and quasi-stable aluminosilicate minerals, the structures of which are sensitive to chemical treatment. In the present study, solid-state 27Al and 29Si nuclear magnetic resonance (NMR) spectra of allophane samples were monitored as they went through several purification procedures. It was confirmed that no significant structural changes were caused by boiling with 6% H2O2 to remove organic matter, by size fractionation (sonification), by sedimentation, by precipitation at pH 4.0, or by dithionite-citrate-bicarbonate treatment for the removal of Fe (hydr)oxides. Hot 5% Na2CO3 treatment for the removal of reactive silica-alumina gels and adsorbed citrate from allophane samples, however, decreased signal intensity corresponding to imogolite-like Si (Q33VIAl, −78 ppm in 29Si NMR) and increased signal intensities corresponding to IVAl (55 ppm in 27Al NMR) and possibly X-ray amorphous aluminosilicates (centered at −85 ppm in 29Si NMR). Cold (room temperature) 5% Na2CO3 treatment for 16 h proved to be effective in avoiding these structural changes.