Inadequate intake of lutein is relevant to a higher risk of age-related eye diseases. However, lutein has been barely incorporated into foods efficiently because it is prone to degradation and is poorly bioaccessible in the gastrointestinal tract. Microfluidics, a novel food processing technology that can control fluid flows at the microscale, can enable the efficient encapsulation of bioactive compounds by fabricating suitable delivery structures. Hence, the present study aimed to evaluate the stability and the bioaccessibility of lutein that is encapsulated in a new noodle-like product made via microfluidic technology. Two types of oils (safflower oil (SO) and olive oil (OL)) were selected as a delivery vehicle for lutein, and two customized microfluidic devices (co-flow and combination-flow) were used. Lutein encapsulation was created by the following: (i) co-flow + SO, (ii) co-flow + OL, (iii) combination-flow + SO, and (iv) combination-flow + OL. The initial encapsulation of lutein in the noodle-like product was achieved at 86.0 ± 2.7%. Although lutein’s stability experienced a decreasing trend, the retention of lutein was maintained above 60% for up to seven days of storage. The two types of device did not result in a difference in lutein bioaccessibility (co-flow: 3.1 ± 0.5%; combination-flow: 3.6 ± 0.6%) and SO and OL also showed no difference in lutein bioaccessibility (SO: 3.4 ± 0.8%; OL: 3.3 ± 0.4%). These results suggest that the types of oil and device do not affect the lutein bioaccessibility. Findings from this study may provide scientific insights into emulsion-based delivery systems that employ microfluidics for the encapsulation of bioactive compounds into foods.