To boost the local microalgae sector, Switzerland needs to better understand the current state of the industry, which is not fully represented in the existing literature. Only by identifying the strengths and weaknesses of the Swiss microalgae industry, will the country be able to develop strategies toward a strong and sustainable sector in the future. This work provides the first structured assessment of Switzerland’s fragmented and poorly documented microalgae sector through desktop research and an online survey of the country’s microalgae stakeholders. First, research articles with Swiss authors and patents with Swiss applicants were mapped. Then, a survey consisting of 8 questions was designed to gather information about the location, purpose, employees, production capacity, activities, and installations of 42 organizations with a research and/or commercial focus. The growing number of organizations working with microalgae in Switzerland is dominated by small companies (<50 employees) that provide services rather than biomass or bioproducts. Microalgae biomass production is about 2 tons DW per year and is also dominated by small-scale producers (<100 kg DW per year). One third of Swiss companies that sell microalgae-based products produce their own biomass abroad or purchase from abroad. Our findings highlight the growth potential of the Swiss microalgae sector. This systematic summary of research interests, technological innovations, and current market parameters is the first step toward future improvements in the sector.