Urban community gardeners create important habitats for pollinators in cities through their gardening practices. In a collaborative research project in 33 community gardens in Berlin and Munich, we examined the link between pollination and garden features under real-life conditions. We aimed to collaboratively develop insect conservation interventions to enhance pollinator diversity and harvest success simultaneously. Most citizen science participants consistently conducted fruit production measurements of their study plants. Nevertheless, the data showed a trade-off between a protocol designed to interfere as least as possible with the gardener's routine and the data’s fit for purpose regarding the research question. Our main lessons learned were (1) to invest in establishing and maintaining a good relationship with participants and (2) to develop hypotheses and methods in close collaboration with participants. We believe it is crucial to foster the integration of different perspectives and knowledge in order to realize the potential of citizen science in pollinator research.