Digital Innovation Units (DIUs) have become an important vehicle for digital innovation and the exploration of new ventures, often applying Design Thinking (DT). However, scholars lack knowledge about how to measure these activities from the perspective of both DIUs and DT. To understand the key challenges involved, an exploratory qualitative research design and a grounded theory approach were adopted to analyze data obtained from interviews conducted with 20 DIU members. Our findings identify eight challenges around the topic of misalignment between the DIUs’ objectives and how their activities are assessed by using metrics. The rich descriptions provided in this study deepen our understanding of the challenges involved in measuring DIUs’ activities, and provide the basis for future developments to monitor and steer their innovation activities more meaningfully to guide resource allocation.