We quantified the amount of habitat loss directly related to the construction of PV power facilities with different size classes and estimated their siting attributes using recent construction patterns at the national scale in Japan and South Korea. Compared to large solar PVs, medium solar PV installations resulted in a higher area loss of semi-natural habitats, including secondary/planted forests, secondary/artificial grasslands, and agricultural lands. The siting attributes of medium and large solar PV facilities further indicated a preferred economic cost-based site selection rather than prioritizing habitat protection for biodiversity conservation. Moreover, even conservation areas were developed when economic and topological conditions were suitable for energy production. Our model simulations indicated that enhanced solar PV construction in urban areas could help to reduce the loss of natural and semi-natural habitats. To increase the renewable energy share while mitigating impacts on biodiversity, our results highlight a proactive assessment to enforce sustainable site-selection criteria for solar PVs in renewable energy initiatives. The revised criteria should consider the cumulative impacts of a broad size class of solar power facilities, including medium PVs, and diverse aspects of the ecological values of natural and semi-natural habitats.