Botulinum neurotoxins (BoNTs) are responsible for botulism, a paralytic disease which can be lethal if not treated in time. They act by entering neurons and targeting the SNARE proteins (Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptor), which in turn blocks neurotransmission. However, these toxins can be repurposed for therapeutic use to treat a large number of conditions. The most studied serotypes are A and E (BoNT/A and BoNT/E, respectively), with notable differences in duration of action and domain spatial organisation. It has been shown that these toxins only exert their activity if the pH drops to 5 or lower, but it is unclear what effect the pH environment has on the toxin which drives this. Currently, the only available structural information on BoNTs is from X-ray crystallography which fixes the protein into a rigid crystal lattice. This gives limited information on its flexible regions, and no information about its dynamics and solution behaviour. To gain insight into this, molecular dynamic (MD) simulations were conducted under varying pH conditions. For BoNT/E, these simulations revealed a shift in conformational populations in solvated systems at pH ≤ 5 when compared to simulations at pH > 5, with the protein adopting a more extended conformation in the former. This was confirmed by analytical ultra-centrifugation (AUC), while small-angle X-ray scattering (SAXS) validated the two major conformations observed in the MD simulations. For BoNT/A, a major conformational change was not observed, but a rare event was identified by MD (in 0.014% of frames studied) which may explain the longer onset of action compared to BoNT/E. Another key difference between the two structures of BoNT/E and BoNT/A is the large number of contacts between a conserved region termed the “switch” and the binding domain (BD) in BoNT/A, which are absent in BoNT/E.