An elaboration of the photonic based sensors is the most promising direction in modern analytical chemistry from the point of view of real clinical applications. The highest sensitivity is demonstrated by sensors based on photonic integrated circuits (PICs). This type of sensor has been recently successfully combined with microfluidics, which decreased the analyte volume for analysis down to microliter units. The most significant disadvantage regarding these photonic sensors is low specificity. One of the methods that could be useful for such type of problem is the layer by layer (LBL) assembly. The peculiarity of a PIC based sensor is the ability to precisely control surface modification by using measurements of a minimum resonance position shift. The bovine serum albumin (BSA) and tannic acid (TA) molecules were selected for LBL assembly because on one side they form a stable LBL assembly film based on hydrogen bonds, while the other side of both TA and BSA molecules can be used for conjugation with target molecules. A microring resonator (MRR) and a Mach-Zehnder interferometer (MZI) based on a silicon nitride platform combined with a microfluidic system were elaborated and used for monitoring the LBL film assembly. Obtained results have a good correlation with measurements carried out by atom force microscopy. Thus, the ability of using PIC based sensors for in situ control of surface modification was demonstrated and can be considered in point-of-care (POC) devices that have a very good perspective for both early pathological state diagnosis and evaluation of treatment efficiency.