Aiming at the enhancement of food products' nutritional and health value, the incorporation of nutraceuticals has attracted increasing interest in the last years. However, they often exhibit low water solubility and stability, limiting their direct incorporation into food products. Also, they show very low bioavailability due to limited bioaccessibility, poor absorption and/or chemical transformation within the gastrointestinal tract. This renders their health benefits extremely difficult to be realized by the consumers. In the present review the recent innovations regarding the formulation and design of bio-based micro and nano-delivery systems to encapsulate nutraceuticals is discussed; it also gives an overview of the challenges associated to their development; and highlights some strategies to enhance nutraceuticals' bioavailability. An insight about delivery systems' potential toxicity (in particular at nano-scale) is also provided. Recent developments in the design of bio-based delivery systems offer the possibility of stabilizing and enhancing nutraceuticals' functionality within food products. In fact, different strategies can be used to enhance nutraceuticals' bioavailability: i) nano-delivery systems, besides showing a huge potential for the protection of valuable nutraceuticals during food processing/digestion, can be used to increase their bioavailability; ii) absorption enhancement technologies have been successfully used to increase nutraceuticals' membrane permeation; and iii) excipient foods have been shown to improve nutraceuticals' biological activity. However, the application of these enabling technologies to food is hindered by very pertinent issues that can be summarized in the effective preservation/maximization of the nutraceuticals' bioactivity and safety, once inside the human body. •Delivery systems allow nutraceuticals' protection and their incorporation in foods.•Bio-based delivery systems can be specifically designed to enhance nutraceuticals' bioavailability.•Bioavailability enhancement strategies include nano-delivery systems, absorption enhancers and excipient foods.•It is crucial to evaluate the safety of nano-delivery systems in food.•Development of delivery systems that provide nutraceuticals' greatest functionality and safety remains a challenge.