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The demand for high-energy and high-power energy storage devices motivates the search for electrode materials with both high capacity and fast ion transport. One class of materials that could achieve such performance are oxides containing crystallographic shear (CS) planes. Here, we compare the structural dynamics of tungsten trioxide (WO 3 ) and its oxygen deficient, CS Magnéli phase (WO 2.9 ) during electrochemical insertion of H + and Li + ions using a combined experimental and computational study. We found that WO 3 inserts more H + per formula unit than WO 2.9 yet operando electrochemical atomic force microscopy shows more deformation in WO 2.9 than WO 3 per inserted H + . In contrast, WO 2.9 accommodates ∼0.2 more Li + per formula unit than WO 3 and has higher Li + diffusion and better rate capability. Operando electrochemical X-ray diffraction shows that Li + insertion into WO 2.9 leads to lattice contraction and 5 % volume change up to Li 0.6 WO 2.9 followed by a zero-strain region up to Li 1.4 WO 2.9 . We find that the presence of CS planes, and its effect on octahedral tilting, lead to different outcomes depending on the inserting ion: while octahedral tilting and lack of CS planes promote H + insertion into WO 3 , their absence in WO 2.9 favor Li + insertion. We propose that the presence of CS planes impart structural rigidity, enabling higher capacity, improved rate capability, and enhanced cyclability during Li + insertion but remove favorable bridging oxygen sites for H + insertion. • H + insertion is suppressed in WO 2.9 due to the absence of octahedral tilting and bridging oxygen sites. • Li + insertion is enhanced in WO 2.9 relative to WO 3. • DFT calculations reveal a wider range of energetically favorable Li + insertion sites in WO 2.9 than WO 3 . • Operando EC-AFM reveals that WO 2.9 undergoes greater deformation than WO 3 during H + insertion. • Operando EC-XRD shows fewer phase transitions in WO 2.9 during Li + insertion.