Guaraná (Paullinia cupana) is a fruit native to the Amazon rainforest recognized by the high levels of phenolic compounds, catechin, and epicatechin in the seeds. However, these phenolic compounds are sensitive to light and heating. In addition, catechin shows astringent sensation, which may limit its application in food. In this way, encapsulation is an alternative to protect bioactive compounds, improve their release into the intestine and mask undesirable sensorial aspects. The aim of this work was to compare the release of phenolic compounds, catechin, and epicatechin in encapsulated or free guarana seed extract (GSE) under simulated gastrointestinal fluids (SGF). Atomized GSE (2.5%, 5% and 7.5% w/w) was dispersed into molten vegetable fat at 64 ºC. The dispersion was atomized using a spray chiller equipped with a cold chamber at 13 °C. Solid lipid microparticles (SLM) were characterized with regard to total phenolic, catechin and epicatechin. In addition, the release levels of bioactive compounds in SLM or free GSE under simulated gastrointestinal fluids were evaluated, as well as the morphology of SLM was analyzed by optical microscopy. The contents of phenolic compounds in the GSE were approximately 400 mg of Gallic Acid Equivalent (GAE)/g of powder, besides 130 mg of catechin and 320 mg of epicatechin per gram of powder. In relation to the gastrointestinal assay, at initial time unencapsulated GSE released 38.8% of the total phenolic compounds. After 4 h under simulated gastrointestinal fluids, only 18.8% of the total phenolic compounds were detected. Regarding encapsulated GSE, at least 52.7% of phenolic compounds, 21% of catechin and 14.8% of epicatechin were released in the formulation with 2.5% of GSE. The formulation containing 7.5% of GSE were more effective to release phenolic compounds (60.3%), catechin (61.0%) and epicatechin (68.0%). The micrographs showed that the SLM were typical spheres, at the initial time of the gastrointestinal assay. SLM were broken in the presence of the simulated intestinal fluid containing bile salts and enzymes that hydrolyze fat. In short, encapsulation improved the controlled release of the bioactive compounds avoiding its degradation when compared to the free GSE. These results encourage the use of spray chilling technology to produce new ingredients.