Microstructured optical waveguides (MOW) are of great interest for chemical and biological sensing. Due to the high overlap between a guiding light mode and an analyte filling of one or several fiber capillaries, such systems are able to provide strong sensitivity with respect to variations in the refractive index and the thickness of filling materials. Here, we introduce a novel type of functionalized MOWs whose capillaries are coated by a layer-by-layer (LBL) approach, enabling the alternate deposition of silica particles (SiO2) at different diameters—300 nm, 420 nm, and 900 nm—and layers of poly(diallyldimethylammonium chloride) (PDDA). We demonstrate up to three covering bilayers consisting of 300-nm silica particles. Modifications in the MOW transmission spectrum induced by coating are measured and analyzed. The proposed technique of MOW functionalization allows one to reach novel sensing capabilities, including an increase in the effective sensing area and the provision of a convenient scaffold for the attachment of long molecules such as proteins.