This paper is focused on the in-line monitoring of the secondary drying phase of a lyophilization process. An innovative software sensor is presented to estimate reliably the residual moisture in the product and the time required to complete secondary drying, that is, to reach the target value of the residual moisture or of the desorption rate. Such results are obtained by coupling a mathematical model of the process and the in-line measurement of the solvent desorption rate and by means of the pressure rise test or another sensors (e.g., windmills, laser sensors) that can measure the vapor flux in the drying chamber. The proposed method does not require extracting any vial during the operation or using expensive sensors to measure off-line the residual moisture. Moreover, it does not require any preliminary experiment to determine the relationship between the desorption rate and residual moisture in the product. The effectiveness of the proposed approach is demonstrated by means of experiments carried out in a pilot-scale apparatus: in this case, some vials were extracted from the drying chamber and the moisture content was measured to validate the estimations provided by the soft-sensor.