Lippia citriodora has been demonstrated to have a wide variety of phytochemicals which provide benefits to human health acting as antioxidants or anti-obesogenics. In this study, these phytochemicals were recovered using a microwave-assisted technology and applying optimal conditions and microencapsulated using spray drying. In this study, two different carbohydrates, maltodextrin (MD) and inulin (IN), were compared as carriers in the encapsulation procedure. The spray drying process was optimized by using a response surface methodology (RSM) based on a central composite design 22, where air inlet temperature and the sample:encapsulating agent ratio (S:EA) were selected as independent variables. Both designs were analyzed equally to evaluate differences between each carrying agent on polar compounds’ encapsulation (process yield (Y%), encapsulation efficiency (EE%) and recovery of compounds (R%)) during the spray drying. The EE% and R% of each polar compound was monitored by High Performance Liquid Chromatography coupled to Time-of-Flight mass spectrometer by electrospray interface (HPLC-ESI-TOF-MS). The results showed that the use of IN as a carrier increased the powder recovered and the recovery of polar compounds after the spray dry process, whereas MD achieved a higher encapsulation efficiency.