The interactions between bottom-up initiatives and top-down structures in the implementation of regional development policies and projects are complex in theoretical and practical terms. Using concepts such as transformative social innovation, adaptive governance, and bridging institutions, we developed an analytical framework to enhance understanding of the processes by which local top-down and bottom-up forces enhance sustainable rural development by co-developing bottom-linked governance. Bottom-linked governance is a multi-level middle ground where actors from various political levels, geographical scales and industry sectors come together to share decision-making. Social innovation has the potential to be transformative, but to do this, it has to be able to scale-up and provoke changes in the governance system. Using a rural social innovation initiative in Costa Rica, we tested our framework and considered the enabling factors of bottom-linked governance. They comprise the various bridging roles the initiative must play: network enabler; knowledge broker; resource broker; transparency and conflict resolution agent; and shared vision champion. We also considered the critical success factors of bottom-linked governance. Bottom-linked governance and social innovation together comprise how planning practice contributes to social-ecological regional development. Sharing of power and participatory decision-making facilitate more flexible, inclusive and effective planning. Our analytical framework was helpful in understanding how a social innovation initiative fostered transformation and contributed to sustainable rural development.