The current study focuses on analyzing the impact of integrating an optical sorter in a seed-separation technological flow, in terms of increasing the quality of the maize seeds appropriate for sowing. The study showed that there are situations when the use of optical separation may result in a number of difficulties in removing a variable rate of good seeds from the raw mass, which can bring economic disadvantages. The identified issue encouraged the development of several flow assessment approaches in order to determine the problem’s essence and to develop the best strategy for action. The key finding was that the evaluated optical sorting equipment cannot eliminate impurities without also removing good seeds, resulting in every 1% increase in impurity level and a rate of 0.70% of the good seeds lost. Therefore, farmers must carefully consider the scenarios where integrating optical sorting into their technological flow is a suitable option, considering the input material quality, the selling price of the product, and the risk of missing an important quantity of high-quality seeds. The working method described may be of significant importance to other farmers who intend to choose the components of grain-cleaning processes effectively.