Non‐vascular photoautotrophs (NVP), including bryophytes, lichens, terrestrial algae, and cyanobacteria, are increasingly recognized as being essential to ecosystem functioning in many regions of the world. Current research suggests that climate change may pose a substantial threat to NVP, but it is highly uncertain to what extent this will affect the associated ecosystem functions and services. Here, we propose a research agenda to address this urgent question, focusing on physiological and ecological processes that link NVP to ecosystem functions while also taking into account the substantial taxonomic diversity across multiple ecosystem types. Accordingly, we developed a new categorization scheme, based on microclimatic gradients, which simplifies the high physiological and morphological diversity of NVP and worldwide distribution with respect to several broad habitat types. We found that habitat‐specific ecosystem functions of NVP will likely be substantially affected by climate change, and more quantitative process understanding is required on (1) potential for acclimation (2) response to elevated CO2 (3) role of the microbiome and (4) feedback to (micro)climate. We suggest an integrative approach of innovative, multi‐method laboratory and field experiments and eco‐physiological modelling, for which sustained scientific collaboration on NVP research will be essential.