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Climate change adaptation is increasingly concerned with how organisations develop capacity to adapt to uncertain futures. A participatory action research project conducted in Victoria, Australia, examined how health and social service organisations developed their organisational adaptive capacity through the use of adaptation decision-support tools. It can be challenging for any organisation to select and apply a decision-support tool, but this is particularly the case where resources and capacities are limited. For most organisations, climate change is only one of a complex set of dynamic stressors they must consider in meeting organisational goals. This paper shows that while decision-support tools can help co-generate knowledge and facilitate customised organisational adaptation processes, for them to be practically helpful for organisations with limited resources and capacities, intensive collaborative and discursive processes are needed to adjust such tools to fit specific organisational contexts and needs. Facilitators and participatory approaches that enable co-inquiry can play a critical role in supplementing scarce resources and initiating adaptation processes that go well beyond the scope and purpose of the decision-support tool used. Organisations working effectively with decision-support tools to adapt to climate change will need to feel ownership of them and have confidence in modifying them to suit their particular adaptation needs and organisational goals.