Amblyopia is a disorder of neurodevelopment that occurs when there is discordant binocular visual experience during the first years of life. While treatments are effective in improving visual acuity, there are significant individual differences in response to treatment that cannot be attributed solely to difference in adherence. In this considerable variability in response to treatment, we argue that treatment outcomes might be optimized by utilizing deep phenotyping of amblyopic deficits to guide alternative treatment choices. In addition, an understanding of the broader knock-on effects of amblyopia on developing visually-guided skills, self-perception, and quality of life will facilitate a whole person healthcare approach to amblyopia.