Photo-based surveys are widely applied to elicit landscape preferences and to assess cultural ecosystem services. Variations in weather and light conditions can potentially alter people’s preferences, as sunny landscapes are more positively perceived than those under inclement weather conditions. To assure comparability across pictures, studies usually include photographs taken at sunny days (i.e., blue sky). However, the influence of clouds in sunny landscapes on people’s preferences has been rarely considered, although color contrasts between clouds and the blue sky may attract people’s attention. This study therefore aimed to assess the effects of clouds in landscape photographs on people’s preferences by (1) examining differences in preference between pairs of landscape photographs (i.e., with clouds and without clouds), and (2) explaining variations through variables from eye-tracking simulation, photo content analysis, and Geographic Information System (GIS)-based analysis. Our results indicate no significant differences in preferences between pictures with and without clouds when the pictures with clouds contained a proportion of sky around 22% and a cloud cover of about 39%. However, a higher proportion of sky positively influenced landscape preferences, while a higher proportion of clouds, especially in combination with a lower proportion of sky, had negative effects. These findings suggest that landscape preference studies should pay attention not only to the appearance of the sky in terms of cloudiness, but they also should control the proportion of sky across different pictures to obtain comparable results. Future research should address limitations regarding the transferability of our findings to other types of landscapes and regarding potential differences in perceptions between respondents with different socio-cultural characteristics. Moreover, landscape preferences under changing weather conditions or different cloud types as well as diurnal and seasonal changes should be further explored.