Background/Objectives: Studies using optical coherence tomography angiography (OCTA) have revealed that individuals recovering from COVID-19 have a reduced retinal vascular density (VD) and larger foveal avascular zones (FAZs) than healthy individuals, with more severe cases showing greater reductions. We aimed to examine aspects of the retinal microvascularization in patients with post-COVID-19 condition (PCC) classified by COVID-19 severity and how these aspects relate to cognitive performance. Methods: This observational cross-sectional study included 104 PCC participants from the NAUTILUS Project, divided into severe (n = 59) and mild (n = 45) COVID-19 groups. Participants underwent cognitive assessments and OCTA to measure VD and perfusion density (PD) in the superficial capillary plexus (SVP) and FAZ. Analysis of covariance and partial Pearson and Spearman correlations were used to study intergroup differences and the relationships between cognitive and OCTA variables. Results: Severe PCC participants had significantly lower central (p = 0.03) and total (p = 0.03) VD, lower central (p = 0.02) PD measurements, and larger FAZ areas (p = 0.02) and perimeters (p = 0.02) than mild cases. Severe cases showed more cognitive impairment, particularly in speed processing (p = 0.003) and executive functions (p = 0.03). Lower central VD, lower central PD, and larger FAZ areas and perimeters were associated with worse executive function performance in the entire PCC sample and in the mild COVID-19 group. Conclusions: Retinal microvascular alterations, characterized by reduced VD and PD in the SVP and larger FAZ areas, were associated with cognitive impairments in PCC individuals. These findings suggest that severe COVID-19 leads to long-lasting microvascular damage, impacting retinal and cognitive health.