Tyndallization presents potential as a cost-effective alternative sterilisation method for small-scale producers. This research aimed to assess the effectiveness of tyndallization at various temperatures in sterilising pempek, a composite food product, and its impact on product quality. The study employed the SDS-PAGE technique to investigate protein polymerisation mechanisms and FTIR to evaluate protein structure, colour, pH, and texture changes. The results indicated protein polymerisation occurred, evidenced by a decrease in Molecule High Chain (MHC) and an increase in actin, corresponding to the rising temperature and tyndallization cycles with a sinusoidal pattern. FTIR spectra demonstrated that the β-helix structure dominated secondary protein structures, consistently observed across different levels and temperature variations. This study contributes new insights into applying thermal processes in preparing composite food products. Regarding quality, tyndallization caused a shift towards a more yellow colour in the pempek and a softer texture, although there were no significant pH changes. The alterations in protein patterns resulted from the varying cycles and temperatures experienced during the tyndallization process. The findings suggest that tyndallization can be considered an effective alternative for sterilising composite products like pempek; however, its implementation still requires the appropriate combination of time, temperature, and tyndallization cycles while considering the potential impact on quality changes during the sterilisation process.