Wettability alteration is one of the most promising techniques to enhance oil recovery of mixed- or oil-wet reservoirs. As contact angle decreases within the matrix, the flux of fracture-matrix counter-current imbibition increases significantly. Wettability-altering agents only influence the wettability of a portion of the matrix region, and not necessarily homogenously. The wettability-altering agents in the aqueous phase make both fractures and matrix water-wet. However, the intensity of the alteration gradually reduces with the distance from the fracture-matrix interface. Beyond the fracture-matrix imbibition halos, wettability remains intact. So, this wettability transition zone needs to be considered during the modelling and simulation of multiphase flow in naturally fractured rocks. Utilizing a finite-element-centred-finite-volume (FECFV) numerical approach, we simulated four waterflooding scenarios on a discrete fracture and matrix (DFM) model built based on an outcrop analogue. The scenarios are (1) waterflooding, (2) wettability alteration immediately after the end of the waterflooding in the first scenario, (3) wettability alteration long after the end of the waterflooding in the first scenario, and (3) dynamic wettability alteration. Dealing with a transient/static non-homogenous distribution of contact angle, oil recovery, ensemble relative permeability, fracture-matrix counter-current wetted area and characteristic length, diffusivity, and Peclet number are significantly influenced between the scenarios. The results of this paper highlight the necessity of enabling commercial software to work with non-homogenously assigned transient relative permeability curves.