Transportation projects can have significant impacts on habitat connectivity and wildlife populations. Wildlife crossings can reduce these impacts, while also increasing driver safety. However, incorporating wildlife crossings into transportation projects and funding them can be difficult within existing systems, which are not set up for valuing such investments as part of a comprehensive program of compensatory mitigation. Mitigation credit agreements (MCAs) provide an opportunity to address this problem through opportunities to develop creative and innovative approaches to compensatory mitigation, including wildlife crossing projects. The California Department of Fish & Wildlife has begun to approve MCAs as part of a California law passed in 2016 (AB2087) that established the Regional Conservation Investment Strategy (RCIS) program, including MCAs. Additional legislation passed in 2022 (SB790) directs the Department to develop crediting mechanisms for wildlife crossing projects, in cooperation with Caltrans. California’s Advance Mitigation Program is the first program to establish advance mitigation credits through habitat connectivity mitigation. Our work merges these new legislative efforts and offers a potential solution to the regulatory community in California and beyond to the difficulties associated with implementing wildlife crossings as compensatory mitigation for project impacts through the MCA program. As proposed, MCAs provide a value assessment that can be used to mitigate the predicted impacts of projects in advance of project development and can be an effective mechanism to catalyze connectivity projects. Advance mitigation mechanisms such as MCAs can reduce overall costs of transportation projects through integrated permit reviews and improved coordination. To date, however, there are no common metrics used to quantify the value of habitat connectivity mitigation efforts or the number of credits that such projects could generate, and few pilot studies have been implemented to test their effectiveness. Using an ongoing project on State Route 17 in Santa Clara County, CA as a case study, we examined methods for quantifying habitat connectivity credits and identifying their value through advance mitigation. We assessed which characteristics should be considered valuable in developing a wildlife crossing and how that value can be translated to mitigation credits using an approach based in conservation science. When considering different strategies for developing a wildlife crossing, it is critical to incorporate scientific evidence to assess unknown impacts and to plan for future climate change, which will bring new species and environmental conditions. By using a scientific approach to develop habitat connectivity mitigation, wildlife crossings can be more useful and cost-effective, increasing the long-term success of these projects.