Applying design thinking to the development of sustainability e-learning can help universities offer digital experiences that align with contemporary student preferences. This study explores such premise in three European Higher Education Institutes (HEIs) based in Poland, Germany and Romania. First, 45 interviews with students from the Generation Z cohort (born between 1995 and 2010) were conducted and coded into end-user personas. Next, multidisciplinary teaching teams used those personas in a design-thinking workshop to prototype digital learning activities on sustainability. In this article, we report in details a replicable five-stage research protocol for gathering persona data and a seven-stage instructional design framework that translates such persona insights into e-learning deliverables. Results show that when instructors base their ideation and prototypes on persona-based empathy maps, the education activities are more relevant in context, more interactive, and better aligned with the United Nations Sustainable Development Goal of Quality Education (SDG 4). The contributions of this study are a detailed, evidence-based workflow that can be adapted by any higher education institution, a practical template for persona creation, conceptualisation, and rapid prototyping, and an analysis of the institutional enablers required to scale the approach.