To address grand challenges like climate change, transformative innovation policies (TIPs) are emerging as a framework for societal prosperity. Implemented through various instruments, TIPs may operate in a multi-level governance (MLG) context whereby policies originate at a supra-national level and are directed to national, regional, and local tiers. TIPs also emphasize inclusivity and engagement with marginalized communities. However, practical insights on these aspects for TIPs are limited. This paper therefore investigates how TIP instruments are channeled from a supra-national context to a local one to engage with marginalized communities. Taking Belgium as the setting for our paper, we focus on the European Green Deal as a TIP and the Just Transition Fund as the instrument. Finding a series of barriers that prevent engagement, we identify the key role of inter-organizational relationships (coordination, cooperation, collaboration), especially related to the initial vertical coordination of a TIP instrument. If vertical coordination does not extend to the local level, engagement with marginalized communities is difficult. Opening horizontal relationships to include a broader set of actors in decision-making processes is also important. Consequently, we unpack these barriers and build upon both the TIP and just transition literature by applying the participatory governance school of thought.