In composing multi-thematic questionnaires for the Lolland-Falster Health Study (LOFUS), we faced a range of challenges, for which we found limited guidance in the literature. LOFUS is a household-based population study covering multiple medical and social research areas and targeting the mixed rural-provincial population of 103,000 persons on the Danish islands Lolland and Falster. Households were randomly selected for invitation. In this paper, we describe and discuss challenges in developing the questionnaires related to stakeholders, content of the questionnaire, and the process itself. The development process was characterised by loops of learning and can be described as an iterative and incremental process. We propose recommendations to researchers and administrators involved in similar development processes, including awareness of the non-linearity and complexity of the process, a need for negotiations and navigation among multiple stakeholders, and acknowledgement of pragmatism as an inherent part of decisions made in the process.