Transdisciplinary research and innovation (R&I) efforts have emerged as a means to address challenges to sustainable transformation. One of the main elements of transdisciplinary efforts is the ‘inclusion’ of different stakeholders, values and perspectives in participatory R&I processes. In practice, however, ‘doing inclusion’ raises a number of challenges. In this article, we aim to contribute to re-politicizing inclusion in transdisciplinarity for transformation, by (1) empirically unraveling four key challenges that emerge in the political practice of ‘doing inclusion’, (2) illustrating how facilitators of inclusion processes perform balancing acts when confronted with these challenges, and (3) reflecting on what the unfolding dynamics suggests about the politics of stakeholder inclusion for societal transformation. In doing so, we analyze the transdisciplinary FIT4FOOD2030 project (2017–2020)—an EU-funded project that aimed to contribute to fostering EU R&I systems’ ability to catalyze food system transformation through stakeholder engagement in 25 Living Labs. Based on 3 years of action-research (including interviews, workshops and field observations), we identified four inherent political challenges to ‘doing inclusion’ in FIT4FOOD2030: (1) the challenge to meaningfully bring together powerful and marginalized stakeholders; (2) combining representation and deliberation of different stakeholder groups; (3) balancing diversities of inclusion with directionalities implied by transformative efforts; and (4) navigating the complexities of establishing boundaries of inclusion processes. We argue that by understanding ‘doing inclusion’ as a political practice, necessitating specificity about the (normative) ambitions in different inclusion settings, facilitators may better grasp and address challenges in transdisciplinarity for transformation.