In recent years, starch nanoparticles (SNPs) have attracted growing attention due to their unique properties as a sustainable alternative to common nanomaterials since they are natural, renewable and biodegradable. SNPs can be obtained by the breakdown of starch granules through different techniques which include both physical and chemical methods. The final properties of the SNPs are strongly influenced by the synthesis method used as well as the operational conditions, where a controlled and monodispersed size is crucial for certain bioapplications. SNPs are considered to be a good vehicle to improve the controlled release of many bioactive compounds in different research fields due to their high biocompatibility, potential functionalization, and high surface/volume ratio. Their applications are frequently found in medicine, cosmetics, biotechnology, or the food industry, among others. Both the encapsulation properties as well as the releasing processes of the bioactive compounds are highly influenced by the size of the SNPs. In this review, a general description of the different types of SNPs (whole and hollow) synthesis methods is provided as well as on different techniques for encapsulating bioactive compounds, including direct and indirect methods, with application in several fields. Starches from different botanical sources and different bioactive compounds are compared with respect to the efficacy in vitro and in vivo. Applications and future research trends on SNPs synthesis have been included and discussed.