The present work studied the antibacterial effect of different formulations of Chitosan (Chs); free Thymoquinone (Tq), and Thymoquinone-loaded chitosan nanoparticles (Tq-Chs NPs) on Bombyx mori L. infected by pathogenic bacteria, by evaluating some biochemical aspects of larval haemolymph. Bombyx mori larvae classified into three groups; each group was fed on mulberry leaves treated with one of the formulations (free Tq, free Chs and Tq-encapsulated Chs) with drug concentrations (0.05% and 0.1%). Before being used, the prepared formulations were characterized by size, morphology, encapsulation efficiency; in addition, in vitro drug release experiment was performed. The biochemical results revealed an improvement in the antibacterial and antioxidant activity of the studied formulations, especially with increasing the concentrations compared to control; (Tq-encapsulated Chs) followed by free Chs and free Tq revealed highly significant decreases in mixed function oxidase (MFO) activity, especially larvae treated with the high concentration (0.1%). The activity of acid phosphatase, total lipid content and carbohydrates pointed to a highly significant increase. Similarly, the qualitative analysis of silkworm proteins showed an obvious variation in the number and position of the detected protein bands from one treatment to another. It can be concluded that Tq and Chs showed an inhibitory impact against pathogenic bacteria infecting Bombyx mori larvae, proved their effects as antioxidant and anti-inflammatory agents which could be improved by loading Tq on Chs nanoparticles (Tq-Chs NPs).