This article aims to investigate the impact exerted by different types of covering an atrium with glazing on the energy performance of a kindergarten building, provided by the authors as a conceptual design. The considered types of atria included an open atrium, a glazed atrium, and an atrium that operated as a hybrid system. Additionally, the following aspects were taken into consideration: the effect of a glazing-integrated PV system (BIPV); the variety of thermal features represented by the inner boundary between the conditioned and the unconditioned space (Uiu); and the atrium space air-exchange ratio (nue) on the energy balance of the building. Energy performance indicators, including energy demands for space heating and cooling (Eu), delivered energy (Ed), and primary energy (Ep) indicators for heating and cooling mode were estimated for the moderate climates and two locations of the building model, i.e., for Warsaw (Central Poland) and Ahlbeck (Northern Germany). The research results prove that the glazed atrium exerts the most beneficial impact on the energy performance of the building. Nevertheless, certain variables must be considered, especially the air-exchange ratio of the atrium space, as they significantly influence the total annual energy performance. The results obtained with regard to the effect exerted by the presence of BIPV systems differ from those usually expected. This is due to the effect of the total solar-energy-transmittance value (g) modulation caused by the system and, finally, by a significant reduction in passive solar-gain harvesting, which is important for heating-mode results in examined climate conditions. Taking the present analysis into account, it can be concluded that the energy and environmental effects of the glazed integrated PV systems in temperate climates are strongly influenced by the environmental conditions, and, in some cases, these solutions may prove to be not efficient enough in terms of the energy and costs.