Microalgae and cyanobacteria represent a diverse renewable resource with significant potential for the industrial production of goods and services with high added value. However, scientific, technical/technological, legislative and market gaps and barriers still limit the growth of these markets in Europe and the number of exploited species. We conducted an in-depth survey of European microalgae researchers, experts and stakeholders to identify these limitations and to discuss strategies, recommendations and guidelines to overcome these barriers. Here, we present the findings of this study which detail the main promising markets for microalgae and cyanobacteria in the coming decades, an updated SWOT analysis of the sector, the current opportunities, limitations, risks and threats for microalgae research and market sectors in Europe, a traffic light analysis for a quick assessment of market opportunities for each microalgae sector and detailed recommendations/guidelines for overcoming the scientific, technical/technological, legislative and market gaps and barriers.