Poly(ethylene terephthalate) (PET) is a polymer of significant industrial importance due to its outstanding physical and chemical properties, making it a key material in various sectors. While PET plays a crucial role in modern applications, its environmental persistence underscores the need for sustainable management and recycling strategies. Enzymatic degradation, particularly through cutinases derived from Fusarium species, has emerged as a promising approach for PET biodegradation. Cutinases from Fusarium oxysporum (FoCut5a) and Fusarium solani (FsCut1) demonstrate the ability to hydrolyze PET into monomers, offering a potential sustainable solution for plastic waste management. In this study, molecular dynamics (MD) simulations were conducted to analyze the structural changes in FoCut5a and FsCut1. To explore the structural rearrangements, we conducted a Free Energy Landscape (FEL) analysis, which revealed that the dynamics of the flap helix and binding loop (residues 74–93 and 172–192 respectively) of FoCut5a allow it to exist in both open and closed states, whereas FsCut1 predominantly adopts a closed state. This difference in conformational dynamics has significant implications for enzymatic efficiency, as the transition between open and closed states facilitates substrate binding and product release. Additionally, scanning electron microscopy (SEM) provided insights into the interaction of F. oxysporum with PET surfaces, further highlighting its biodegradation potential. Understanding the mechanistic basis of PET degradation by cutinases is important for engineering enzyme systems to enhance PET degradation and improve the turnover of specific products, offering valuable insights for the development of biotechnological strategies aimed at sustainable materials management in the context of plastic waste recycling.