Context. Clouds play an important role in the radiative transfer of planetary atmospheres because of the influence they have on the different molecular signatures through scattering and absorption processes. Furthermore, they are important modulators of the radiative energy budget affecting surface and atmospheric temperatures.Aims. We present a detailed study of the thermal emission of cloud-covered planets orbiting F-, G-, K-, and M-type stars. These Earth-like planets include planets with the same gravity and total irradiation as Earth, but can differ significantly in the upper atmosphere. The impact of single-layered clouds is analyzed to determine what information on the atmosphere may be lost or gained. The planetary spectra are studied at different instrument resolutions and compared to previously calculated low-resolution spectra.Methods. A line-by-line molecular absorption model coupled with a multiple scattering radiative transfer solver was used to calculate the spectra of cloud-covered planets. The atmospheric profiles used in the radiation calculations were obtained with a radiative-convective climate model combined with a parametric cloud description.Results. In the high-resolution flux spectra, clouds changed the intensities and shapes of the bands of CO2 , N2 O, H2 O, CH4 , and O3 . Some of these bands turned out to be highly reduced by the presence of clouds, which causes difficulties for their detection. The most affected spectral bands resulted for the planet orbiting the F-type star. Clouds could lead to false negative interpretations for the different molecular species investigated. However, at low resolution, clouds were found to be crucial for detecting some of the molecular bands that could not be distinguished in the cloud-free atmospheres. The CO2 bands were found to be less affected by clouds. Radiation sources were visualized with weighting functions at high resolution.Conclusions. Knowledge of the atmospheric temperature profile is essential for estimating the composition and important for avoiding false negative detection of biomarkers, in both cloudy and clear-sky conditions. In particular, a pronounced temperature contrast between the ozone layer and surface or cloud is needed to detect the molecule. Fortunately, the CO2 bands allow temperature estimation from the upper stratosphere down to the troposphere even in the presence of clouds.