Aim This study aimed to evaluate the protective effect of flaxseed mucilage on the co-extrusion microencapsulation of Lactobacillus rhamnosus GG. Methods Core flow rate, chitosan coating, and flaxseed mucilage concentration were optimised for the microencapsulation of L. rhamnosus. The microbeads were characterised and evaluated on microencapsulation efficiency and cell released after 6 h of sequential digestion. Results The optimised parameters for the L. rhamnosus microencapsulation were 1.0 mL/min core flow rate, 0.4% (w/v) chitosan coating, and 0.4% (w/v) flaxseed mucilage. The L. rhamnosus microbeads with flaxseed mucilage in core and wall materials had a smooth surface with 781.3 mu m diameter, the highest microencapsulation efficiency (98.8% w/w), lowest swelling (5196.7% w/w) and erosion ratio (515.5% w/w), and least cell release (<40% w/w) with 9.31 log(10) CFU mL(-1) after sequential digestion. Conclusions This study showed the protective capacity of flaxseed mucilage towards the L. rhamnosus GG during microencapsulation and gastrointestinal environment.