In this study, a modular, multi-step, photometric microflow injection analysis (micro-FIA) system for the automatic determination of Cu(II) in a bioreactor was developed. The system incorporates diverse 3D-printed modules, including a platform formed by a mixer module to mix Cu(II) with hydroxylamine, which reduces Cu(II) to Cu(I) linked to a diluter module via a Tesla valve, a chelation mixer module, a disperser module, and a detector module provided by an LED light source at λ = 455 nm and a light dependence resistor (LDR) as a light intensity detector. The system measures the color intensity resulting from the chelation between Cu(I) and neocuproine. The micro-FIA system demonstrated good capability for automatic and continuous Cu(II) determination, in a wide range of Cu concentrations, from 34 to 2000 mg L−1. The device exhibits a good repeatability (coefficient of variation below 2% across the measured concentration range), good reproducibility, and has an accuracy of around 100% between 600 and 1900 mg L−1. Real samples were analyzed using both the micro-FIA system and an atomic absorption spectroscopy method, revealing no statistically significant differences. Additionally, a Tesla valve located before the detector substituted a 3-way solenoid valve, eliminating the need for moving parts.