We explored the influence of D₂O on the fibrillation kinetics and structural dynamics of amyloid intrinsically disordered proteins (IDPs), including α-synuclein, amyloid-β 1–42, and K18. Our findings revealed that fibrillation of IDPs was accelerated in D₂O compared to that in H₂O, exhibiting faster kinetics in contrast to the structured protein, insulin. Structural investigations using electrospray ionization ion mobility mass spectrometry and small-angle X-ray scattering combined with molecular dynamics simulations demonstrated that IDPs did not show significant structural changes that could influence accelerated fibrillation in D₂O. Umbrella sampling of protein protofibrils verified that an increased level of hydrogen bonding of D₂O and enhanced hydrophobic interactions stabilized β-sheet structured fibrils in D₂O. These findings indicate that stabilizing β-sheet fibrils and a more hydrophobic microenvironment in D₂O result in enhanced and faster fibrillation of IDPs. The study highlights the importance of considering D₂O’s differential impact on protein interactions when conducting structural and kinetic analyses, particularly for native peptides and proteins.