Microalgal biomass can be used to derive many different types of biofuels. In order to widely commercialize this technology, its limitations and weaknesses must be eliminated. Many technical and economic issues also need to be clarified and unknowns answered. Microalgae-based technologies have been shown to be versatile, efficient and suitable for practical and commercial use. However, the current technological readiness level (TRL) of most microalgae-based bioenergy production systems precludes their quick and widespread implementation. Their development is limited by a combination of factors that must be precisely identified, after which their negative impact on scale-up prospects can be eliminated or minimized. The present study identifies the main barriers to the development of industrial microalgae-production and microalgae-to-biofuel systems. In addition, it proposes measures and efforts necessary to achieve a higher TRL, which will provide investors with sought-after performance and cost-efficiency data for the given project. The main barriers to the development of microalgae cultivation and processing systems have been identified to include: the complex nature of the cultivation process with multiple variables involved; lack of sufficient data from pilot-scale and near-full-scale plants, which often precludes reliable life cycle assessment (LCA); and insufficient legal assistance, advisory assistance, subsidies and funding for innovative projects. Potential ways of improving performance and competitiveness of microalgae-based systems include: process optimization techniques, genetic engineering, yield improvement through advanced process control and monitoring, use of waste as feedstock and dedicated support programs. The presented summary of the current stage of microalgal biofuel production technology development indicates the directions for further research and implementation work, which are necessary for the final verification of the application potential of these solutions.