Research to isolate seaweed bioproducts and identify their health-promoting effects is gaining increasing attention due to their potent antimicrobial, anti-inflammatory and antioxidant properties. This study describes the positive effect of particle size reduction, validated by different seaweed examples, in boosting the extraction yields of bioactive compounds, when utilized in conjunction with innovative, short-duration, green heating protocols (i. e subcritical water extraction (SBWE). In these validation protocols, we optimized the recovery of antibacterial, antioxidant and anti-inflammatory bioactivities from 2 different macroalgal species; brown algae (Phaeophyceae ex: Ascophyllum nodosum) and green algae (Chlorophyta ex: Ulva lactuca). Different hot extraction protocols were applied to extract different particle sizes (ranging from fine to coarse: <25; 25–53; 53–106; 106–355; >355 μm) of powdered seaweed samples. The obtained results demonstrated that the highest extraction yields of total carbohydrates, glucuronic acid, phenolics and flavonoids, as well as antioxidant, antimicrobial and anti-inflammatory activities were obtained with microwave protocols for a defined time using the particle sizes of 25–53 μm. Furthermore, we confirmed the safety profile of seaweed extracts on RAW 264.7 cells and verified by measuring the Transepithelial Electrical Resistance (TEER) of Caco-2 monolayer cultures. In conclusion, our study confirmed the efficacy of the optimized green extraction approach in the preparation of safe and valuable bioactive compounds that could be used in the development of seaweed-based functional foods and nutraceuticals.