There is a significant trend towards the integration of natural substances with bio-polymers for fully bio-based functional composites. Polylactic acid is regarded as a promising biodegradable polymer for replacing synthetic polymers. Differing from the case of natural fiber, the incompatibility of polylactic acid with bio-based molecules prevents it from being used to fabricate high-quality sustainable composites. This work presents a simultaneous ultraviolet shielding and antibacterial finishing process of polylactic acid combined with bioactive baicalin and an eco-friendly ester, which is highlighted for (a) the lack of synthetic chemicals involved in such process, (b) adsorption enhancement achieved at a mild temperature, and (c) marginal color change on treated polylactic acid. A response surface methodology was adopted to analyze the impacts of various factors on the baicalin quantity in polylactic acid, and to optimize the treatment condition. The uptake ratio of baicalin in polylactic acid was drastically promoted from 8.5 mg/g to 21.1 mg/g using methyl cinnamate. The response surface methodology based on a central composite design experiment indicated that the usage of baicalin was the most significant factor followed by methyl cinnamate and temperature. After optimization, a very faint color depth of 1.2 was apparent, but UPF 50+ and 92% bacterial reduction could be achieved. In all, the success in strengthening of the functionalities of polylactic acid extends the applications of polylactic acid products.