Conjugation of protein therapeutics with polymers like polyethylene glycol (PEG) has been shown to increase their therapeutic efficiency. However, manufacturing of PEGylated drugs requires an additional, carefully controlled reaction step after purifying the protein, followed by further purification of over- and under-PEGylated variants. In this work, we have used a combined spectroscopic and statistical approach for monitoring and control of the PEGylation reaction for G-CSF using near infrared spectroscopy (NIRS). An online NIRS probe deployed in the reaction vessel has been used to track conversion of G-CSF into monoPEGylated and multiPEGylated forms using calibrated partial least squares regression models on the NIRS spectra which are collected in real time every 3 s. A pH probe integrated with a peristaltic pump facilitates automated quenching of the reaction at the targeted time. The NIRS spectra have also been used to build a batch evolution model for the reaction from end-to-end, including the addition of the reactants to the reaction vessel, the progress of the reaction for 70 min, and the final quenching with Tris base. Online spectra are compared against the statistical process control charts of the batch evolution model in real time to detect deviations as soon as they occur. The system was demonstrated for four common deviations in the PEGylation process, namely: delayed quenching time, wrong concentration of reducing agent added, wrong PEG to G-CSF ratio, and wrong sequence of addition of reactants. The system was able to identify all four deviations in real time and alert the operator to take control actions. The PAT approach suggested here embraces the quality by design framework and can be generalized for manufacturing scale monitoring and control of different biotechnology reactions with spectroscopic signatures.