Obesity and overweight lead to adverse metabolic effects on blood pressure, cholesterol, triglycerides and insulin resistance. To overcome this problem, the present study was carried out to develop capsaicin loaded nanoparticles based polymeric microneedle patches for transdermal delivery. The extracted capsaicin from Capsicum annuum L. was formulated as nanoparticles using clove oil, ethanol, PEG 400 and sodium caseinate. The nanoparticles were 106.8 nm in size with a zeta potential of −50.8 mV and polydispersity index (PDI) of 0.314, confirmed by DLS. The size and spherical morphology were confirmed further by SEM and TEM analysis. With an encapsulation efficiency of 95%, X-ray diffraction analysis of nanoparticles revealed 45% crystallinity and 54% amorphous properties. DSC profiles verified an endothermic peak with a melting point of 140.34 °C, and FTIR spectroscopy confirmed strong bonding between nanoparticles. The plasma bioavailability of capsaicin in nano-formulation was higher compared to native capsaicin in C57BL/6 mice. In vitro and ex vivo release kinetics of capsaicin from MNPs were maximum at 3 min. Thus, the transdermal delivery of capsaicin via microneedle patches will aid in converting WAT to BAT, specifically in those obese populations without the need for strenuous physical exercise and dietary restriction.