Cystinosis is a rare lysosomal storage disease characterised by cystine crystal formation within cells. In the eyes, crystals accumulate in the cornea causing photophobia, loss of visual acuity, and corneal complications. Strict adherence to topical cysteamine treatment is the only therapy that reduces corneal crystal accumulation. Cystinosis, a crystallopathy, is also a disease of inflammation. As the disease progresses the inflammatory processes have a greater impact on the ocular manifestations. The age at which inflammation becomes increasingly significant is dependent on the adequacy of early patient management and adherence with therapy. As patients are living longer with cystinosis, optimising ocular management is increasingly important. No clinical guidelines addressing the long-term ocular management of cystinosis exist. Similarly, there is little recognition in the literature of how to address the inflammatory component of the disease. This paper presents management guidelines, linked to the 3C Classification of severity, used at our centre that provides a framework for optimising care. Adoption of these can help preserve the sight of cystinosis patients. The paper also hypothesises the molecular pathway leading to corneal inflammation.