New strategies to synthesize nanometer-scale silicon dioxide (SiO2) patterns have drawn much attention in applications such as microelectronic and optoelectronic devices, membranes, and sensors, as we are approaching device dimensions shrinking below 10 nm. In this regard, sequential infiltration synthesis (SIS), a two-step gas-phase molecular assembly process that enables localized inorganic material growth in the targeted reactive domains of polymers, is an attractive process. In this work, we performed in situ Fourier transform infrared spectroscopy (FTIR) measurements during SiO2 SIS to investigate the reaction mechanism of trimethylaluminum (TMA) and tri(tert-pentoxy) silanol (TPS) precursors with polymers having ester functional groups (poly(methyl methacrylate) (PMMA), poly(ethyl methacrylate) (PEMA), polycaprolactone (PCL), and poly(t-butyl methacrylate) (PBMA)), for the purpose of growing patterned nanomaterials. The FTIR results show that for PMMA and PEMA, a lower percentage of functional groups participated in the reactions and formed weak and unstable complexes. In contrast, almost all functional groups in PCL and PBMA participated in the reactions and showed stable and irreversible interactions with TMA. We discovered that the amount of SiO2 formed is not directly correlated with the number of interacting functional groups. These insights into the SiO2 SIS mechanism will enable nanopatterning of SiO2 for low-dimensional applications.