Many studies have analysed the effects that design elements, such as lighting and colour, have on students’ cognitive functions. These analyses, while providing useful information, do not allow researchers to compare the effects of multiple design elements. The objective of the present study is to analyse the relative influence of lighting, colour and geometry on attention and memory, the main cognitive functions that underlie learning, and on preference. In a controlled, virtual reality (VR)-based experiment, 200 university students (100 male/100 female) performed attention, memory and preference tests in classrooms with different configurations of lighting (colour temperature and illuminance), colour (saturation and hue) and geometry (height and width). The results identified significant gender-based differences, which demonstrates the need to segment, by gender, samples in this type of study. Lighting had the greatest influence, significantly affecting males’ memories, females’ attention and the preferences of both genders. Colour was also an influential element, significantly affecting females’ attention, while geometry was the least influential. Finally, it should be highlighted that attention was the metric most sensitive to design variations. These results may be of interest to architects, interior designers and engineers who wish to create classrooms that satisfy students’ psychological needs.