The aim of this study was to evaluate the effect of soaking seeds in hot water on the content of selected bioactive compounds in alfalfa sprouts. Temperature and time regimes were: 85 °C, for 10 and 40 s; 90 °C and 100 °C, for 10 s. Sprouts were examined for the contents of ascorbic acid, chlorophylls a and b, α- and β-carotene, neoxanthin, violaxanthin, lutein and total phenolics. In most cases, the treatment applied had no significant effect on the contents of lutein, violaxanthin, neoxanthin, β-carotene and total phenolics. However, disinfection at 100 °C caused a significant reduction in ascorbic acid content, an increase in total phenolic content and a rise in the proportion of cotyledons in the mass of sprouts. The treatment variants applied did not significantly affect the total chlorophyll content in cotyledons. This study revealed that seed treatment with hot water may, depending on the applied parameters, affect sprout morphology, ascorbic acid content and total phenolic content.