Fructose is a carbohydrate with essential applications in the food industry, mainly due to its high sweetness and low cost. The present investigation focused on optimising fructose production from commercial inulin using the enzymatic immobilisation method and applying the response surface methodology in a 12-run central composite design. The independent variables evaluated were the pH (−) and temperature (°C). The substrate consisted of a commercial inulin solution at a concentration of 1 g/L, while the catalyst consisted of the enzyme inulinase from Aspergillus niger (EC 232-802-3), immobilised in 2% m/v sodium alginate. A stirred vessel reactor was used for 90 min at 120 rpm, and quantification of reducing sugars was determined using DNS colorimetric and UV–Vis spectrophotometric methods at a 540 nm wavelength. After applying the response surface methodology, it was determined that the catalytic activity using the immobilisation method allows for a maximum total productivity of 16.4 mg/h under pH and temperature of 3.9 and 37 °C, respectively, with an efficiency of 96.4%. The immobilised enzymes’ reusability and stability compared to free enzymes were evaluated, obtaining activity up to the fifth reuse cycle and showing significant advantages over the free catalyst.