Micronutrients, as essential components of prenatal care, are important to reduce the risk for maternal and child morbidity and mortality by lowering pregnancy-related complications. The present study aimed to investigate the status of the trace elements, i.e., selenium, zinc, and manganese in pregnant and non-pregnant women from a developing country and to evaluate its relationship with maternal and child complications. Selenium, zinc, and manganese concentrations were measured in the blood serum of 80 pregnant women and compared with 40 non-pregnant healthy controls. The quantitative analyses of trace elements were performed by using the inductively coupled plasma–optical emission spectrometry (ICP-OES) method. The information about the dietary habits of the study participants was recorded by using a food frequency questionnaire. The results showed significant lower selenium and zinc levels in pregnant women as compared to the controls (2.26 ± 1.09 vs. 2.76 ± 1.15 µmol/L, p = 0.031; 21.86 ± 7.21 vs. 29.54 ± 7.62 µmol/L, p < 0.001) respectively, with no difference in manganese concentrations (1.40 ± 0.09 vs.1.38 ± 0.09 log10 nmol/L, p = 0.365). Regarding maternal and child complications, higher manganese levels were associated with an increased odds ratio for maternal complications (OR = 3.175, CI (95%) 1.631−6.181; p = 0.038). Consumption of dairy products was associated with lower selenium and manganese values. Pregnant women showed a lower serum selenium and zinc status, and in addition elevated serum manganese concentrations, which might be associated with a higher risk for maternal pregnancy/birth complications, although more studies are necessary to evaluate this association.