Disclosed herein are methods for the isolation and purification of a botulinum neurotoxin (BoNT) protein, or a polypeptide comprising a receptor binding domain of BoNT, from a solution. The method comprises contacting the solution containing the protein or polypeptide to a matrix which has attached thereto a non-toxic non-hemagglutinin (NTNHA) under conditions appropriate for binding, washing the matrix to thereby remove unbound materials, and eluting the protein or polypeptide with a solution that dissociates the bound protein from the NTNHA. Conditions appropriate for binding are a pH of less than 7.5 (e.g, 6). Conditions appropriate for dissociation are a pH greater than or equal to 7.5 (e.g., 8). Compositions specific to the methods are also disclosed.