The Cell microencapsulation has been used in a wide variety of biological or medical researches. There are many types of natural or synthetic polymers that have been used to encapsulate living cells. Among them, collagen is a frequently used hydrogel for the microencapsulation of cells mainly because of its excellent biocompatibility and biodegradability properties. Compared with the conventional cell microencapsulation methods, the utilization of microfluidic-based methodology can realize microbead generation in a more uniform and continuous manner. However, most of the proposed devices are not only technically demanding but might also be harmful to the encapsulated cells. These can hamper the subsequent application of cell-encapsulated microbeads. To tackle these issues, this study reports a spotting-based microfluidic device for continuous generation of cell-encapsulated collagen microbeads. The working principle is mainly based on the use of a pneumatically driven micro-vibrator to continuously generate tiny cells/collagen microdroplets in a thin oil layer. The temporarily formed collagen microdroplets soon sink into the sterile, and biocompatible Pluronic® F127 suspension (25 °C, 8% (v/v)) that stably maintains the shape of the collagen microdroplets during thermal gelation process. In this study, the size and uniformity of the collagen microbeads were regulated by the input flow rate of collagen suspension and the pulsing frequency of the micro-vibrator. Within the experimental conditions studied, the proposed method was able to generate collagen microbeads ranging from 73.9–353.4 μm in diameter with high uniformity (Coefficient of variation (CV): 6.8%–7.4%). Results also exhibited that the encapsulated 3T3 cells kept at a high cell viability of 96 ± 2%, suggesting that the proposed cell microencapsulation process is cell friendly. As a whole, the proposed device has opened up a route to generate collagen microbeads or microencapsulation of cells in a simple, continuous, controllable, uniform, and cell-friendly manner with less contamination.