Well-designed and supported innovation niches may facilitate transitions towards sustainable agricultural futures, which may follow different approaches and paradigms such as agroecology, local place-based food systems, vertical farming, bioeconomy, urban agriculture, and smart farming or digital farming. In this paper we consider how the existing agricultural innovation systems (AIS) approach might be opened up to better support the creation of innovation niches. We engage with Innovation Ecosystems thinking to consider the ways in which it might enhance efforts to create multi-actor, cross-sectoral innovation niches that are capable of supporting transitions to sustainable agricultural systems across multiple scales. While sharing many similarities with AIS thinking, Innovation Ecosystems thinking has the potential to broaden AIS by: emphasizing the role of power in shaping directionality in innovation platforms or innovation communities that are connected to niches and their interaction with regimes; highlighting the plurality of actors and actants and the integral role of ecological actants in innovation; and offering an umbrella concept through which to cross scalar and paradigmatic or sector boundaries in order to engage with a variety of innovation systems affecting multifunctional agricultural landscapes and systems. To this end, an Agricultural Innovation Ecosystems approach may help design and support development of transboundary, inter-sectoral innovation niches that can realize more collective and integrated innovation in support of sustainability transitions, and help enact mission oriented agricultural innovation policy.