The effect of near-complete deoxygenation and polar species removal on the deposition propensity of a Jet A-1 fuel type with marginal thermal oxidative stability was studied in a laboratory-scale approach. The fuel deoxygenation was carried out via nitrogen purging, and two types of bespoke zeolites were used separately in a packed bed reactor for partial polar separation. The treated fuel samples were assessed individually for deposition propensity, using a "high Reynolds thermal stability (HiReTS)" test device. It was found that when the concentration of hydroperoxides in fuel is relatively high, the polar removal is a more effective way than fuel deoxygenation in reducing carbonaceous deposits. Furthermore, competitive adsorption of dissolved O-2 with polar species was studied for a model fuel doped with a few polar species, as well as for the Jet A-1 with marginal thermal stability, in the packed bed reactor with zeolite 3.7 A. The polar species added to the model fuel share the same functional groups as those in Jet A-1 with a strong impact on fuel thermal degradation and surface deposition. These include hexanoic acids, hexanol, hexanal, hexanone, phenyl amine (aniline), butylated hydroxytoluene, dibutyl disulfide, and Fe naphthenate. A one-dimensional model for the calculation of dissolved O-2 adsorption in the packed bed reactor was built using COMSOL Multiphysics. The modeling results were in good agreement with the induction period prior to the beginning of the O-2 adsorption, as well as the different stages of O-2 uptake during the competitive adsorption between dissolved O-2 and polar species in the Jet A-1 fuel. The calculation showed a discrepancy with the experimental results beyond the second phase of O-2 adsorption. More theories, assumptions, and physical submodels are required to build a more robust predictive model. A new chemical reaction pathway based on the self-reaction of hydroperoxides was proposed as part of "basic autoxidation scheme" to justify the relatively high deposition propensity of the marginal fuel after near-complete deoxygenation. The viability of this reaction pathway was supported by the quantum chemistry calculations.