Nickel refining company Norilsk Nickel Harjavalta Oy (NNH) produces the following three main types of nickel products: cathode nickel, nickel powders (briquettes), and nickel salts. The key role in achieving high performance and guaranteed quality of nickel products is played by the distribution of impurities, in particular, selenium, and the control of their behavior. Selenium exerts a sharply negative effect on the formation of a cathode nickel base. At high concentrations in a nickel–cobalt solution, this impurity makes it impossible to produce stable commercial nickel cathodes. The study of the behavior of selenium in the circuit of processing metallurgical middlings, such as the converter matte and matte of slag-cleaning electric furnaces (SCFs), allowed us to make certain changes to the technological scheme of the NNH leaching shop and to clarify the parameters of the main operations. A hypothesis is proposed about a possible mechanism of the effect of the metallized fraction (alloy) contained in the initial raw materials on the reduction of Se6+ to Se4+. Our experiments confirm a direct relation between the degree of selenium precipitation from a solution into a solid precipitate and the alloy content in the initial raw materials. It is shown that a combination of the SCF matte with the converter matte and/or the nickel concentrate (NC) from converter matte separation can be used to effectively control the distribution of selenium in the NNH technology by preventing its critical concentrations in a nickel catholyte. The experimental research are used to develop a two-flow scheme for processing molten products; this scheme uses a combination of NC and products with a high metallized fraction content. This method allowed us to minimize the selenium concentration of in the nickel catholyte.