The growing availability of high-resolution biodiversity data is enhancing our ability to implement biodiversity conservation more effectively. Spatial planning has widely utilized such fine-scale biodiversity data, and proposals of finely-organized protected area networks have been increasing. However, a naive adoption of such fine-scale data for conservation may not only degrade the utility of the data, but may even risk reduction of long-term efficacy of conservation efforts. This is due to inherent tradeoffs between the efficacy of conservation actions over short-term and its persistence over long-term that is characterized by the management scale of spatial planning associated with the resolution of the data used. To demonstrate this argument, the spatiotemporal ecosystem dynamics must be described, but such discussions are limited in the literature. Here, we discuss the potential issues associated with naive uses of fine-scale biodiversity data to establish fine-tuned spatial planning. We then emphasize the importance of matching the data resolution with an appropriate scale of spatial planning that is realized by transforming the data resolution. This method is readily applicable for widely used decision-support tools for spatial planning. A simple worked example is provided to demonstrate its utility with a long-term conservation efficacy in spatial planning. Guided by the recent explosion of biological data, our discussion provides new insights into the ways to maximize the utility of these data, and further improve biodiversity conservation.