In the current debate surrounding the biopsy-free diagnosis of CeD, it is crucial to identify factors influencing the accuracy of results. This study investigated the impact of total IgA on the non-invasive diagnosis of celiac disease (CeD). We retrospectively assessed total IgA titers' influence on the diagnostic accuracy of different tTG-IgA thresholds compared to the upper reference value (UNL). Of 165 included patients, tTG-IgA values at 10× UNL and 6× UNL showed specificity of 82.6% and 73.9% and sensitivity of 49.3% and 69.0%, respectively, in predicting intestinal villous atrophy (Marsh 3). In 130 patients, total IgA levels were known at baseline. These patients were divided into three tertiles according to total IgA, i.e., patients with lower, intermediate, or higher total IgA within the population. For patients with total IgA ≥ 245 mg/dL, using a tTG-IgA cutoff of 6× UNL instead of 10× UNL resulted in decreased specificity from 71.4% to 42.8% and increased sensitivity from 67.6% to 81.1%. For patients with total IgA < 174 mg/dL and between 174 mg/dL and 245 mg/dL, using a tTG-IgA cutoff of 6× UNL instead of 10× UNL maintained specificity (75.0% and 85.7%, respectively) with increased sensitivity (from 46.2% to 64.1% and from 36.1% to 52.8%, respectively). In conclusion, total IgA influences the diagnostic accuracy of a predetermined tTG-IgA cutoff. Greater consideration should be given to total IgA, beyond its deficiency, in evaluating the applicability and accuracy of non-invasive CeD diagnosis.