Systematic uncertainties in the mass measurement of galaxy clusters limit the cosmological constraining power of future surveys that will detect more than 10 5 clusters. Previously, we argued that aperture masses can be inferred more accurately and precisely than 3D masses without loss of cosmological constraining power. Here, we use the Baryons and Haloes of Massive Systems (BAHAMAS) cosmological, hydrodynamical simulations to show that aperture masses are also less sensitive to changes in mass caused by galaxy formation processes. For haloes with 𝑚 200m,dmo > 10 14 ℎ −1 M , binned by their 3D halo mass, baryonic physics affects aperture masses and 3D halo masses similarly when measured within apertures similar to the halo virial radius, reaching a maximum reduction of ≈ 3 per cent. For lower-mass haloes, 10 13.5 < 𝑚 200m,dmo /ℎ −1 M < 10 14 , and aperture sizes ∼ 1 ℎ −1 cMpc, representative of weak lensing observations, the aperture mass is consistently reduced less ( 5 per cent) than the 3D halo mass ( 10 per cent for 𝑚 200m ). The halo mass reduction evolves only slightly, by up to 2 per centage points, between redshift 0.25 and 1 for both the aperture mass and 𝑚 200m . Varying the strength of the simulated feedback so the mean simulated hot gas fraction covers the observed scatter inferred from X-ray observations, we find that the aperture mass is consistently less biased than the 3D halo mass, by up to 2 per centage points at 𝑚 200m,dmo = 10 14 ℎ −1 M . Therefore, cluster aperture mass calibrations provide a fruitful path forward for future cluster surveys to reduce their sensitivity to systematic uncertainties.