Dental resin composites are widely used in clinical settings but often face longevity issues due to the development and accumulation of microcracks, which eventually lead to larger cracks and restoration failure. The incorporation of microcapsules into these resins has been explored to introduce self-healing capability, potentially extending the lifespan of the restorations. This study aims to enhance the performance of self-healing dental resins by optimizing the microcapsules–resin matrix physicochemical interactions. Poly(urea–formaldehyde) (PUF) microcapsules were reinforced with melamine and subsequently subjected to surface functionalization with 3-aminopropyltriethoxysilane (APTES) and (3-mercaptopropyl)trimethoxysilane (MPTMS). Additionally, microcapsules were functionalized with a bilayer approach, incorporating tetraethyl orthosilicate (TEOS) with either APTES or MPTMS. X-ray photoelectron spectroscopy (XPS) and thermogravimetric analysis (TGA) confirmed an increased Si:C ratio from 0.006 to 0.165. The functionalization process did not adversely affect the structure of the microcapsules or their healing agent volume. Compared to PUF controls, the functionalized microcapsules demonstrated enhanced healing efficiency, with TEOS/MPTMS-functionalized microcapsules showing the highest performance, showing a toughness recovery of up to 35%. This work introduces a novel approach to functionalization of microcapsules by employing advanced silanizing agents such as APTES and MPTMS, and pioneering bilayer functionalization protocols through their combination with TEOS.