Retrievals of trace gas concentrations from satellite observations are mostly performed for clear regions or regions with low cloud coverage. However, even fully clear pixels can be affected by clouds in the vicinity, either by shadowing or by scattering of radiation from clouds in the clear region. Quantifying the error of retrieved trace gas concentrations due to cloud scattering is a difficult task. One possibility is to generate synthetic data by three-dimensional (3D) radiative transfer simulations using realistic 3D atmospheric input data, including 3D cloud structures. Retrieval algorithms may be applied on the synthetic data, and comparison to the known input trace gas concentrations yields the retrieval error due to cloud scattering. In this paper we present a comprehensive synthetic dataset which has been generated using the Monte Carlo radiative transfer model MYSTIC (Monte Carlo code for the phYSically correct Tracing of photons In Cloudy atmospheres). The dataset includes simulated spectra in two spectral ranges (400–500 nm and the O2A-band from 755–775 nm). Moreover it includes layer air mass factors (layer-AMFs) calculated at 460 nm. All simulations are performed for a fixed background atmosphere for various sun positions, viewing directions and surface albedos. Two cloud setups are considered: the first includes simple box clouds with various geometrical and optical thicknesses. This can be used to systematically investigate the sensitivity of the retrieval error on solar zenith angle, surface albedo and cloud parameters. Corresponding 1D simulations are also provided. The second includes realistic three-dimensional clouds from an ICON large eddy simulation (LES) for a region covering Germany and parts of surrounding countries. The scene includes cloud types typical of central Europe such as shallow cumulus, convective cloud cells, cirrus and stratocumulus. This large dataset can be used to quantify the trace gas concentration retrieval error statistically. Along with the dataset, the impact of horizontal photon transport on reflectance spectra and layer-AMFs is analysed for the box-cloud scenarios. Moreover, the impact of 3D cloud scattering on the NO2 vertical column density (VCD) retrieval is presented for a specific LES case. We find that the retrieval error is largest in cloud shadow regions, where the NO2 VCD is underestimated by more than 20 %. The dataset is available for the scientific community to assess the behaviour of trace gas retrieval algorithms and cloud correction schemes in cloud conditions with 3D structure.