In mesoscale and global atmospheric simulations with large horizontal domains, strong horizontal flow across the grid is often unavoidable, but its effects on cloud‐topped boundary layers have received comparatively little study. Here the effects of cross‐grid flow on large‐eddy simulations of stratocumulus and trade‐cumulus marine boundary layers are studied across a range of grid resolutions (horizontal × vertical) between 500 m × 20 m and 35 m × 5 m. Three cases are simulated: DYCOMS nocturnal stratocumulus, BOMEX trade cumulus, and a GCSS stratocumulus‐to‐trade cumulus case. Simulations are performed with a stationary grid (with 4–8 m s−1 horizontal winds blowing through the cyclic domain) and a moving grid (equivalent to subtracting off a fixed vertically uniform horizontal wind) approximately matching the mean boundary‐layer wind speed. For stratocumulus clouds, cross‐grid flow produces two primary effects on stratocumulus clouds: a filtering of fine‐scale resolved turbulent eddies, which reduces stratocumulus cloud‐top entrainment, and a vertical broadening of the stratocumulus‐top inversion which enhances cloud‐top entrainment. With a coarse (20 m) vertical grid, the former effect dominates and leads to strong increases in cloud cover and LWP, especially as horizontal resolution is coarsened. With a finer (5 m) vertical grid, the latter effect is stronger and leads to small reductions in cloud cover and LWP. For the BOMEX trade cumulus case, cross‐grid flow tends to produce fewer and larger clouds with higher LWP, especially for coarser vertical grid spacing. The results presented are robust to choice of scalar advection scheme and Courant number.