In this study, we eliminated the microbiota of the gut of Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae) via starvation. We then compared the initial responses of the cellulase system and symbiotic reproduction in termites fed filter paper treated with either antimicrobials or distilled water. Three key findings were as follows: (a) an antibiotic mixture of ampicillin and kanamycin significantly depressed reproduction of Holomastigotoides mirabile Koidzumi and Spirotrichonympha leidyi Koidzumi but promoted reproduction of Pseudotrichonympha grassii Koidzumi during 12 to 48 h of feeding, (b) the enzyme activity levels of three cellulases did not correspond to the respective protozoan levels and did not vary directly with the numeric increase of protozoa in either treatment, and (c) in the antibiotics treatment, β-glucosidase (BG, 0–48 h) and cellobiohydrolase (CBH, 0–12 h) activity levels between endogenous (salivary gland/foregut and midgut) and exogenous (hindgut) origin were negatively correlated. Both the activity level (6–48 h) and expression amounts (6–12 h) of endogenous endo-β-1, 4-glucanase was significantly higher in antibiotics treatment. Before initiation of feeding (0 h), BG and CBH activities had relative maximum levels when the protozoa population was at its minimum. These findings suggest that C. formosanus possesses an endogenous compensation mechanism which functions when the symbiotic cellulolytic system is impaired.