The commercial reality of bioactive compounds and oil production from microalgal species is constrained by the high cost of production. Downstream processing, which includes harvesting and extraction, can account for 70–80% of the total cost of production. Consequently, from an economic perspective extraction technologies need to be improved. Microalgal cells are difficult to disrupt due to polymers within their cell wall such as algaenan and sporopollenin. Consequently, solvents and disruption devices are required to obtain products of interest from within the cells. Conventional techniques used for cell disruption and extraction are expensive and are often hindered by low efficiencies. Microwave-assisted extraction offers a possibility for extraction of biochemical components including lipids, pigments, carbohydrates, vitamins and proteins, individually and as part of a biorefinery. Microwave technology has advanced since its use in the 1970s. It can cut down working times and result in higher yields and purity of products. In this review, the ability and challenges in using microwave technology are discussed for the extraction of bioactive products individually and as part of a biorefinery approach.