In the context of global efforts to conserve and promote biodiversity, urban environments play a crucial role due to their significant impact on natural ecosystems. Japan offers a particularly relevant case for exploring strategies that enhance urban biodiversity, given the cultural importance of nature and the distinctive characteristics of Japanese urban fabric, largely shaped by private development which determines the localized and individual character of spatial initiatives; as many industrialized societies, Japan also faces challenges in maintaining connections with nature. This paper investigates architectural and urban design approaches that enable the integration of small, fragmented private urban spaces into urban-scale green infrastructure, exploring also how these areas can provide cultural ecosystem services in daily life. The study adopts a mixed methodology, combining a policy review—focusing on national biodiversity strategies and micro-greening subsidies—with a qualitative analysis of 38 small green spaces adjacent to private residences in three Tokyo neighborhoods, aimed to assess their ecological, spatial, and socio-cultural value. Findings suggest that coordinated public policies and subsidized private greening efforts with architectural design interventions can transform small-scale non-built urban spaces in at least three typologies of “setback gardens” part of the city’s ecological networks, supporting biodiversity and enhancing the spatial and socio-cultural quality of the urban environment.