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A method for the determination of phosphorus in mineralized biodiesel using a micro-flow-batch analyzer (μFBA) with solenoid micro-pumps was proposed. The samples were mineralized using an ashing procedure at 550 °C followed by dissolution of the residue. The determination of phosphorus was performed by employing the well-known molybdenum blue method. The measures of the absorbance were performed at 850 nm using an InfraRed LED integrated into the μFBA. Comparing with the reference method, no statistically significant differences were observed when applying the paired t-test at a 95% confidence level. Recovery study shows results between 97.9% and 105.8%. The proposed microsystem using solenoid micro-pumps presented satisfactory robustness and high sampling rate (190 h −1 ), with satisfactory reproducibility (relative standard deviation n =3), low reagents consumption (32 μL per analysis) and cost to build the device. Moreover, μFBA presents limit of detection (0.014 mg Kg −1 ), precision and accuracy compatible with the biodiesel regulations that establish a maximum concentration of 10 mg Kg −1 (Brazil, USA, EU), suggesting that it is a good alternative for the determination of phosphorus in biodiesel.