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Abstract Bin microphysics schemes are useful tools for cloud simulations and are often considered to provide a benchmark for model intercomparison. However, they may experience issues with numerical diffusion, which are not well quantified, and the transport of hydrometeors depends on the choice of advection scheme, which can also change cloud simulation results. Here, an atmospheric large‐eddy simulation model is adapted to simulate a statistically steady‐state cloud in a convection cloud chamber under well‐constrained conditions. Two bin microphysics schemes, a spectral bin method and the method of moments, as well as several advection methods for the transport of the microphysical variables are employed for model intercomparison. Results show that different combinations of microphysics and advection schemes can lead to considerable differences in simulated cloud properties, such as cloud droplet number concentration. We find that simulations using the advection scheme that suffers more from numerical diffusion tends to have a smaller droplet number concentration and liquid water content, while simulation with the microphysics scheme that suffers more from numerical diffusion tends to have a broader size distribution and thus larger mean droplet sizes. Sensitivities of simulations to bin resolution, spatial resolution, and temporal resolution are also tested. We find that refining the microphysical bin resolution leads to a broader cloud droplet size distribution due to the advection of hydrometeors. Our results provide insight for using different advection and microphysics schemes in cloud chamber simulations, which might also help understand the uncertainties of the schemes used in atmospheric cloud simulations.