The prevalence of allergies is rising every year. For those who suffer from it, ocular inflammation and irritation can be inconvenient and unpleasant. Anti-allergy eyedrops are a readily available treatment for symptoms of ocular allergy (OA) and can help allergy sufferers regain normal function. However, the eye is a delicate organ, and multiuse eyedrops often utilise preservatives to deter microbial growth. Preservatives such as benzalkonium chloride (BAK) have been shown to induce decreased cell viability. Therefore, during a period of high localised inflammation and eye rubbing, it is important that the preservatives used in topical medicines do not contribute to the weakening of the corneal structure. This review explores ocular allergy and the thinning and protrusion of the cornea that is characteristic of the disease keratoconus (KC) and how it relates to a weakened corneal structure. It also describes the use of BAK and its documented effects on the integrity of the cornea. It was found that atopy and eye rubbing are significant risk factors for KC, and BAK can severely decrease the integrity of the corneal structure when compared to other preservatives and preservative-free alternatives.