We aimed to determine the effects of deep learning-based reconstruction (DLR) on radiomic features obtained from cardiac computed tomography (CT) by comparing with iterative reconstruction (IR), and filtered back projection (FBP). A total of 284 consecutive patients with 285 cardiac CT scans that were reconstructed with DLR, IR, and FBP, were retrospectively enrolled. Radiomic features were extracted from the left ventricular (LV) myocardium, and from the periprosthetic mass if patients had cardiac valve replacement. Radiomic features of LV myocardium from each reconstruction were compared using a fitting linear mixed model. Radiomics models were developed to diagnose periprosthetic abnormality, and the performance was evaluated using the area under the receiver characteristics curve (AUC). Most radiomic features of LV myocardium (73 of 88) were significantly different in pairwise comparisons between all three reconstruction methods (P < 0.05). The radiomics model on IR exhibited the best diagnostic performance (AUC 0.948, 95% CI 0.880–1), relative to DLR (AUC 0.873, 95% CI 0.735–1) and FBP (AUC 0.875, 95% CI 0.731–1), but these differences did not reach significance (P > 0.05). In conclusion, applying DLR to cardiac CT scans yields radiomic features distinct from those obtained with IR and FBP, implying that feature robustness is not guaranteed when applying DLR.