Simple and fast photometric flow injection analysis system was developed for sensing of β-1,3-glucan from medicinal mushroom Ganoderma lucidum during fermentation. For this purpose, the chitosan–guar gum–silver nanoparticle–beta glucanase (Ch–GG–AgNPs–βG) beads and Ch–GG–AgNPs–GOD (glucose oxidase) beads were prepared. The bead packed mini-columns were then used to assemble a flow injection analysis (FIA) system for the detection of β-(1 → 3)-d-glucan biomarker or glucose. This colorimetric flow system can detect glucose and glucan with detection limits as low as 50 ng mL⁻¹ and 100 ng mL⁻¹ (S/N = 3), respectively. The analysis time of this FIA was approximately 40 s, which is faster than the previously reported glucan sensors. The glucose and glucan calibration curves were obtained in the range of 0.25–1.25 μg mL⁻¹ (R² = 0.988) and 0.2–1.0 μg mL⁻¹(R² = 0.979), respectively. The applicability of the nano-bio-composite FIA sensor system for spiked and real β-(1 → 3)-d-glucan samples were tested, and the accuracy of the results were greater than 95%. Thus, the designed FIA provides a simple, interference free and rapid tool for monitoring glucose and β-glucan content, which can be used for various food samples with a little modification.