Anthropic activities negatively impact natural and artificial ecosystems, necessitating interdisciplinary mitigation strategies such as multi-species building envelope designs. This paper introduces a computational multi-criteria decision-making (MCDM) methodology to support these envelope designs. We also propose a nested set strategy for key performance indicators (KPI) to strategically measure architectural and ecological performances. We integrate the strategy into a proposed hybrid MCDM methodology using computational design tools. The methodology was tested using a generic volume case study described by an architectural and ecological objective with varied priorities. Initial results highlight the computational interoperability of hybrid MCDM, informed by nested KPI set priorities, as support for multi-species building envelope designs.