(1) Background: Nanocrystals (NCs)-based electrochemical sensors have been proposed for biomarkers detection, although immunosensors using ZnO NCs decorated with copper are still scarce. (2) Methods: Electrochemical immunodetection of human salivary alpha-amylase (HSA) used ZnO, CuO, and ZnO:xCu (x = 0.1, 0.4, 1.0, 4.0, and 12.0) NCs. (3) Results: Substitutional incorporation of Cu²⁺ in the crystalline structure of ZnO and formation of nanocomposite were demonstrated by characterization. Graphite electrodes were used and the electrochemical signal increased by 40% when using ZnO:1Cu and 4Cu (0.25 mg·mL⁻¹), in an immunosensor (0.372 mg·mL⁻¹ of anti-alpha-amylase and 1% of casein). Different interactions of HSA with the alpha-amylase antibody were registered when adding the NCs together, either before or after the addition of saliva (4 μL). The immunosensor changed specificity due to the interaction of copper. The ZnO:1Cu and ZnO:4Cu samples showed 50% interference in detection when used before the addition of saliva. The immunosensor showed 100% specificity and a sensitivity of 0.00196 U·mL⁻¹. (4) Conclusions: Results showed that the order of NCs addition in the sensors should be tested and evaluated to avoid misinterpretation in detection and to enable advances in the validation of the immunosensor.