This study developed a green extraction method using virgin coconut oil and microwave assistance to obtain lutein from marigold flowers, and validated a UHPLC-Q-Orbitrap-HRMS method for lutein quantification. The lutein-rich extract was non-toxic to ARPE-19 retinal pigment epithelial cells at concentrations up to 16 µM, and microencapsulation with a 1:5 oil-to-wall ratio achieved the highest encapsulation efficiency (82.60%). These findings support the potential of microencapsulated marigold extract as a safe functional ingredient for eye health products.