This is the study to find out the method that maximizes the effect of a hair conditioner while minimizing hair damage, by comparing different times to apply a hair conditioner during permanent wave operation. For the experiment, a hair conditioner was applied to four samples of hair with iron permanent wave - with each sample differentiating in the treatment time - and then, the samples were compared in terms of tensile strength, hydration, thickness and properties of the hair shaft as well as changes in the hair cuticle observed by microstructure analysis using Atomic Force Microscope (AFM). The average tensile strength of the sample that was treated in the middle was 3 percent higher than that of the early treated, 11 percent higher than the late treated, 16 percent higher than the non-treated. The mid-treated sample also had the lowest rate in terms of moisture loss. The mid-treated sample had 3 percent higher hydration than the early-treated, and the late-treated sample lost moisture at a 51 percent faster rate than the mid-treated. In the hair shaft`s thickness experiment, the mid-treated sample had the highest average value. The mid-treated sample showed more healthy cuticle than the others with a membrane formed on the surface, in Topography image, 3D-image, and Line-profile analysis of the hair cuticle surface using AFM where the surface, wear on the tip, shade, looseness, and change in thickness were examined. This research could be used for reducing hair damage when applying the hair conditioner in isolation or combination with other chemicals.