A highly sensitive analytical procedure for photometric determination of molybdenum in plant materials was developed and validated. This procedure is based on the reaction of Mo(V) with thiocyanate ions (SCN−) in acidic medium to form a compound that can be monitored at 474 nm and was implemented employing a multicommuted flow analysis setup. Photometric detection was performed using an LED-based photometer coupled to a flow cell with a long optical path length (200 mm) to achieve high sensitivity, allowing Mo(V) determination at a level of μg L−1 without the use of an organic solvent extraction step. After optimization of operational conditions, samples of digested plant materials were analyzed employing the proposed procedure. The accuracy was assessed by comparing the obtained results with those of a reference method, with an agreement observed at 95% confidence level. In addition, a detection limit of 9.1 μg L−1, a linear response (r = 0.9969) over the concentration range of 50–500 μg L−1, generation of only 3.75 mL of waste per determination, and a sampling rate of 51 determinations per hour were achieved.