Organic solvents are commonly used to extract lutein. However, they are toxic and are not environmental-friendly. There are only a few reports on the quantification of lutein. Therefore, this study aimed to determine a suitable extraction method by which to obtain lutein from marigold flower (Tagetes erecta L.), using coconut oil to evaluate the cytotoxicity of extract in ARPE-19 cells, to optimize the encapsulation process for the development of microencapsulated marigold flower extract, and to develop the method for analysis of lutein by using UHPLC-Q-Orbitrap-HRMS. Coconut oil was used for the extraction of marigold flowers with two different extraction methods: ultrasonication and microwave-assisted extraction. The UHPLC-Q-Orbitrap-HRMS condition for the analysis of lutein was successfully developed and validated. Marigold flower extract obtained using the microwave method had the highest lutein content of 27.22 ± 1.17 mg/g. A cytotoxicity study revealed that 16 µM of lutein from marigold extract was non-toxic to ARPE-19 cells. For the development of microencapsulated marigold extract, the ratio of oil to wall at 1:5 had the highest encapsulation efficiency and the highest lutein content. Extraction of lutein using coconut oil and the microwave method was the suitable method. The microencapsulated marigold extract can be applied for the development of functional ingredients.