The edible oils and fats industry is still looking for novel solutions that can reduce the unsaturation of lipids and at the same time maintain low concentrations of trans- and saturated fatty acids. In this work, we adapted a simple method to synthesize amorphous alloy nanocatalysts of nickel and boron (Ni-B), which was used in literature to hydrogenate unsaturated hydrocarbons and the hydrogenated products were reported to have a low concentration of trans-isomers. Soybean oil was hydrogenated with a group of Ni-B alloy catalysts synthesized at various conditions. We report that some Ni-B alloy catalysts showed activities similar to conventional nickel and palladium catalysts, while some did not have activities. The trans-fat contents in products hydrogenated by Ni-B were approximately half of those when the commercial nickel catalyst was used. The selectivities of Ni-B catalysts were also different from the commercial nickel catalyst. We further showed that, although the hydrogenation reaction rate was strongly affected by reaction conditions, the production of trans-fat was primarily affected by the catalyst and secondarily by the studied reaction conditions. Because of the simplicity to synthesize amorphous catalysts, this work may lead to a group of novel nanocatalysts that integrate different functions of various transition metals to synergistically reduce the formation of both trans- and saturated fatty acids in partially hydrogenated edible oils and fats.