Systems change requires complex interventions. Cross-sector partnerships (CSPs) face the daunting task of addressing complex societal problems by aligning different backgrounds, values, ideas and resources. A major challenge for CSPs is how to link the type of partnership to the intervention needed to drive change. Intervention strategies are thereby increasingly based on Theories of Change (ToCs). Applying ToCs is often a donor requirement, but it also reflects the ambition of a partnership to enhance its transformative potential. The current use of ToCs in partnering efforts varies greatly. There is a tendency for a linear and relatively simple use of ToCs that does limited justice to the complexity of the problems partnerships aim to address. Since partnership dynamics are already complex and challenging themselves, confusion and disagreement over the appropriate application of ToCs is likely to hamper rather than enhance the transformative potential of partnerships. We develop a complexity alignment framework and a diagnostic tool that enables partnerships to better appreciate the complexity of the context in which they operate, allowing them to adjust their learning strategy. This paper applies recent insights into how to deal with complexity from both the evaluation and theory of change fields to studies investigating the transformative capacity of partnerships. This can (1) serve as a check to define the challenges of partnering projects and (2) can help delineate the societal sources and layers of complexity that cross-sector partnerships deal with such as failure, insufficient responsibility taking and collective action problems at four phases of partnering.