Lemon thyme contains several bioactive health-promoting compounds of high antioxidant capacity—such as polyphenols, carotenoids, and chlorophyll—which may undergo degradation during drying in incorrect processing conditions. This work is aimed at evaluating the impacts of different drying techniques and parameters on the chemical and physical properties of lemon thyme. In the experiment, lemon thyme leaves are dried using two traditional hot-air methods, convective drying (temperature 70°C or 80°C, air velocity 2 m/s), and fluidized bed drying (temperature 70°C or 80°C, air velocity 5–10 m/s); as well as two innovative drying methods, microwave-assisted fluidized bed (MFB) drying (microwaves at a power of 240 or 440 W, air temperature 40°C, air velocity 5–10 m/s) and microwave-vacuum (MV) drying (microwaves at a power of 240 or 440 W, under vacuum at 4–6 kPa). The kinetics of water delivery are described using the Page Model. After drying, the nutritional composition of the material is analyzed: polyphenol (total content and polyphenols profile by ultra-performance liquid chromatography), carotenoid, and chlorophyll total content, as well as antioxidant capacity (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt [ABTS+] and ferric reducing antioxidant power [FRAP]). Color changes ( L*, a*, b*, ΔE) are also analyzed using the visible effects of lemon thyme pigment disintegration. It is found that the MV drying method is the best for lemon thyme preservation, as it has the shortest process time and the highest retention of polyphenols (78.90%-82.14%), chlorophylls (51.54%-52.68%), antioxidant capacity (47.83%-48.63% of ABTS+ and 20.85%-45.45% of FRAP), and presented the least color change ( ΔE = 25.57-28.32). For preserving carotenoids, the most protective method is MFB (retention 68.46%-70.61 %).