Fungal keratitis is a time-sensitive ocular infection that often requires a high index of suspicion followed by intensive medical/surgical interventions to achieve a successful clinical outcome. COVID-19 pandemic-related restrictions, necessitated the modification of conventional protocols and guidelines associated with the treatment of keratomycosis. We report four cases of atypical fungal keratitis with poorly differentiated clinical characteristics. The challenges faced during their management were (1) the dilemma of clinically differentiating fungal (Scedosporium and Purpureocillium lilacinum) and bacterial keratitis; (2) treatment of Scedosporium and Trichosporon keratitis with natamycin monotherapy; (3) mixed infection of Candida albicans and Aureobasidium pullulans and continuing medications before rescraping the corneal ulcer against the recommended treatment guidelines; (4) phenotypic identification and differentiation among morphologically resembling fungi; and (5) decision making arising out of disparities between KOH and fungal culture results. Three patients responded well to conservative treatments. The fourth patient underwent therapeutic keratoplasty but was lost to follow-up due to travel-related pandemic restrictions. This case series seeks to broaden the clinician's knowledge of rare and emerging moulds as presumptive aetiologies of keratomycosis. It also intends to emphasize the significance of early microbiological investigations, (direct microscopy and culture), in resource-limited settings, for initiating empirical treatment for a better visual prognosis.