(1) Background: COVID-19 had a major impact on cancer diagnostics and treatment. Delays in diagnosis of cutaneous melanoma were particularly feared, given the impact on survival and morbidity that comes with advanced stages. Moreover, its incidence in Belgium has been rapidly increasing in recent decades. This Belgian population-level study quantifies the pandemic effect on the number of melanoma diagnoses and Breslow thickness in 2020 and 2021. (2) Methods: In using an automated algorithm, the number of cutaneous melanoma diagnoses and Breslow thickness were extracted from all pathology protocols from 2017–2021 by the Belgian Cancer Registry. Monthly variations, as well as year-to-year differences, were studied. (3) Results: Annual incidence of cutaneous melanoma fell by 1% in 2020, compared to 2019, mainly due to a diagnostic deficit in March, April, and May 2020. An 8% incidence increase occurred in 2021, primarily reflecting an increase in the number of the thinnest melanomas (≤1 mm). Both the mean and median Breslow thicknesses were higher in spring 2020, resulting from an underrepresentation of thinner tumors. However, no particulars stood out on a full-year basis in either 2020 or 2021. (4) Conclusions: Considering the expected incidence increase, we estimate almost 210 melanoma diagnoses were missed in Belgium in 2020, corresponding to 6% of the expected number. This deficit occurred mainly during the first COVID-19 wave. Despite some rebound, the 2021 total was still 3% short of the expected number, leaving around 325 diagnoses remaining pending in 2020 and 2021, corresponding to a two-year deficit of 4.35%. Fortunately, mainly thin melanomas were missed, without any detectable shift toward thicker tumors later in 2020 and or 2021.