The reduction of aggregate-bitumen bond caused by moisture damage is a major cause of premature failure of asphalt pavement. This failure is mainly caused due to adhesive failure, which involves weakening of bond at aggregate-bitumen interface. This becomes more dominant if bitumen film is thin or improper coating of bitumen over aggregate surface occurs. In conventional mixing of aggregate and bitumen, coarse aggregates receive thin bitumen film as compared to fine aggregates. The large difference among the specific surface area of different sizes of aggregates leads to non-uniform distribution of the binder. To avoid this, a new mixing technique known as “two-phase mixing” was adopted in the study. In this technique, coarse aggregates were initially mixed with the partial binder. After its pre-coating, fines were mixed with it followed by adding remaining binder. A comparison between asphalt mixes prepared using one-phase and two-phase mixing have been done in terms of tensile strength ratio (TSR) and dynamic modulus. These tests were performed at various freeze–thaw (0, 1, 3 and 6) cycles. Also, the effect of moisture conditioning on rheological properties of two-phase mixes were studied and compared with that of conventional one-phase mixes. The moisture resistance of the mixes was compared using a damage factor introduced in sigmoid function adopted for dynamic modulus mastercurve fitting. Using this, the extent of shifting of mastercurve in downward direction was estimated. Both elastic and viscous properties of asphalt mixes were decreased by moisture conditioning. The adopted two-phase was found to produce more moisture resistant asphalt mixes. Lastly, a correlation between TSR and damage factor introduced in sigmoid equation for moisture damage was done, which showed a good correlation.