The integration of spray drying and agglomeration offers significant advantages, such us continuous production with lower energy consumption. However, it is a knife-edge process with a narrow operating window and limited degrees of freedom that decide between successful agglomeration and fluidized bed blockage due to excessive moisture. In this contribution, factors influencing the spray-through agglomeration process of skim milk powder as a model system were investigated via a design of experiments. Three in-line monitoring methods were applied and tested to observe the most important parameters in the agglomeration process—the product moisture and particle size distribution. Regarding the moisture content, a capacitive moisture sensor was calibrated with linear regression and a near-infrared sensor with partial least squares regression. Near-infrared spectroscopy was found to be the suitable method for determining the moisture content, while the capacitive moisture sensor mainly provides information on the bulk density, filling level, or fluidization state in the fluidized bed. Additionally, particle size distribution data were extracted from the spectral data using in-line data from a spatial filter velocimetry probe in the fluidized bed. This opens the potential to monitor both parameters in real time with a single non-invasive sensor.