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Microalgae contain a diverse range of high-value compounds that can be utilized directly or fractionated to obtain components with even greater value-added potential. With the use of microalgae for food and medical purposes, there is a growing interest in their digestive properties and impact on human gut health. The extraction, separation, and purification of these components are key processes in the industrial application of microalgae. Innovative technologies used to extract and purify microalgal high-added-value compounds are key for their efficient utilization and evaluation. This review’s comprehensive literature review was performed to highlight the main high-added-value microalgal components. The technologies for obtaining bioactive compounds from microalgae are being developed rapidly, various innovative, efficient, green separation and purification technologies are emerging, thus helping in the scaling-up and subsequent commercialization of microalgae products. Finally, the digestive behavior of microalgae nutrients and their health effects on the human gut microbiota were discussed. Microalgal nutrients exhibit favorable digestive properties and certain components have been shown to benefit gut microbes. The reality that must be faced is that multiple processes are still required for microalgae raw materials to final usable products, involving energy, time consumption and loss of ingredients, which still face challenges.