This study aimed to characterize micronutrient deficiencies, including iron, ferritin, folic acid, vitamin D, zinc (Zn), vitamin B12, and copper, in patients with celiac disease, and evaluated the effects of these deficiencies on selected hematological parameters, including hemoglobin and mean corpuscular volume (MCV). Celiac disease (CeD), an immune-mediated disorder affecting the small bowel, is associated with genetic factors and micronutrient deficiencies. This meta-analysis was performed in accordance with the PRISMA guidelines. Literature searches of multiple databases retrieved 4140 studies, of which 45 were selected. Risk of Bias was performed in accordance with the STROBE checklist. Meta-analysis revealed a significant difference in hemoglobin levels between patients with CeD and controls (standardized mean difference (SMD) -0.59 (95% confidence interval (CI) -0.8459 to -0.3382); P = 0.0003). Iron levels were lower in patients with CeD (SMD ≈ -0.4 (95% CI -0.7385 to -0.0407); P = 0.0334), as were ferritin (SMD -0.6358 (95% CI -0.8962 to -0.3755); P = 0.0002), folic acid (SMD -0.5446 (95% CI -0.9749 to -0.1142); P = 0.0187), and vitamin D (SMD -0.4011 (95% CI -0.8020 to -0.0001); P = 0.0499) levels, while Zn levels were significantly reduced (SMD -1.1398 (95% CI -2.0712 to -0.2084); P = 0.0242). No significant differences were found in MCV, or copper or vitamin B12 levels between patients with CeD and controls. This study highlighted significantly higher micronutrient deficiencies in patients diagnosed with CeD than in controls, underscoring the importance of systematic nutritional assessment and multidisciplinary management to address micronutrient deficiencies and minimize negative health impact(s).