Purpose: To quantify choriocapillaris flow alterations in patients with pseudoxanthoma elasticum (PXE) in pre-atrophic stages and its association with structural changes of the choroid and outer retina. Methods: Thirty-two eyes of 21 patients with PXE and 35 healthy eyes of 35 controls were included. The density of choriocapillaris flow signal deficits (FDs) was quantified on 6 $times$ 6-mm optical coherence tomography angiography (OCTA) images. Spectral-domain optical coherence tomography (SD-OCT) images were analyzed for thicknesses of the choroid and outer retinal microstructure and correlated with choriocapillaris FDs in the respective Early Treatment Diabetic Retinopathy Study subfield. Results: The multivariable mixed model analysis for choriocapillaris FDs revealed significantly higher FDs associated with the group (PXE patients vs. controls +13.6; 95% confidence interval [CI] 9.87-17.3; P < 0.001), with increasing age (+0.22% per year; 95% CI 0.12-0.33; P < 0.001), and with retinal location (significantly higher FDs in nasal compared to temporal subfields). Choroidal thickness (CT) did not differ significantly between both groups (P = 0.078). The CT and choriocapillaris FDs were inversely correlated (-1.92 µm per %FDs; interquartile range -2.81 to -1.03; P < 0.001). Larger values of the choriocapillaris FDs were associated with significant thinning of the overlying photoreceptor layers (outer segments: -0.21 µm per %FDs, P < 0.001; inner segments: -0.12 µm per %FDs, P = 0.001; outer nuclear layer: -0.72 µm per %FDs; P < 0.001). Conclusions: Patients with PXE display significant alterations of the choriocapillaris on OCTA even in pre-atrophic stages and in the absence of significant choroidal thinning. The analysis favors choriocapillaris FDs over choroidal thickness as a potential early outcome measure for future interventional trials in PXE. Further, increased FDs in nasal compared to temporal locations mirror the centrifugal spread of Bruch’s membrane calcification in PXE.