Marine microalgae and seaweeds (microalgae) represent a sustainable source of various bioactive natural carotenoids, including β-carotene, lutein, astaxanthin, zeaxanthin, violaxanthin and fucoxanthin. Recently, the large-scale production of carotenoids from algal sources has gained significant interest with respect to commercial and industrial applications for health, nutrition, and cosmetic applications. Although conventional processing technologies, based on solvent extraction, offer a simple approach to isolating carotenoids, they suffer several, inherent limitations, including low efficiency (extraction yield), selectivity (purity), high solvent consumption, and long treatment times, which have led to advancements in the search for innovative extraction technologies. This comprehensive review summarizes the recent trends in the extraction of carotenoids from microalgae and seaweeds through the assistance of different innovative techniques, such as pulsed electric fields, liquid pressurization, supercritical fluids, subcritical fluids, microwaves, ultrasounds, and high-pressure homogenization. In particular, the review critically analyzes technologies, characteristics, advantages, and shortcomings of the different innovative processes, highlighting the differences in terms of yield, selectivity, and economic and environmental sustainability.