Some apparently quiescent supermassive black holes (BHs) at centers of galaxies show quasi-periodic eruptions (QPEs) in the X-ray band, the nature of which is still unknown. A possible origin for the eruptions is an accretion disk. However, the properties of such disks are restricted by the timescales of recurrence and the duration of the flares. In this work, we test the possibility that the temporal properties of known QPEs can be explained by accretion from a compact accretion disk with an outer radius out g and we focus on a particular object, GSN 069. We ran several 3D general relativistic magnetohydrodynamic (GRMHD) simulations with the H-AMR code of thin and thick disks and studied how the initial disk parameters such as thickness, magnetic field configuration, magnetization, and Kerr parameter affect the observational properties of QPEs. We show that accretion onto a slowly rotating BH through a small, moderately thin accretion disk with an initially low plasma beta can explain the observed time between outbursts and the lack of evidence for a variable jet emission. In order to form such a disk, the accreting matter should have a low net angular momentum. A potential source for such low angular momentum matter with a quasi-periodic feeding mechanism might be a tight binary of wind-launching stars. Apart from their primary application, our results can also be useful for general studies of systems with small accretion disks, in which evolution occurs very rapidly so that the disks cannot be considered stationary. For such systems, it is important to understand how the initial conditions affect the results.