Supply chains are fundamental to the economic functioning of society, through the assembly and transport of essential goods such as food, clothes and medicine. Technological advancements have driven supply chains to become increasingly automated, to optimise for efficiency and cost, and to respond to disturbances. However, optimising for social concerns is less prevalent. Increasing consumer preferences towards purchasing goods whose production is more aligned with those consumers’ values (such as sustainability), requires values-management capabilities within supply chain software. Such capabilities include tracing, monitoring, and verifying values-alignment between end-consumers and stakeholders. In this paper, we advocate for adaptive values-alignment between end-consumers and stakeholders in cyber-physical supply chains. We motivate this by means of an example of a coffee supply chain, which in turn surfaces social and technical challenges to values-alignment. We then propose a distributed, locally adaptive values-alignment approach. We implement this approach within a software framework and quantitatively illustrate its impact in increasing alignment from two competing perspectives: supply chain stakeholders and end-consumers. We show that end-consumer bias performs better by reducing values-misalignment by up to 85%. We also find that the homogeneity of stakeholders’ values is not correlated with an increase in values-alignment with end-consumers and that mixed values-alignment across the supply chain may be beneficial for supporting stakeholder engagement.