Organic fermented milk products are an area of interest combining functional properties and sustainable practices. Limited information is available regarding the specific components of organic milk that may impact the growth of lactic acid bacteria. This study emphasised the differences in bioactive compounds between organic and conventional milk and their potential influence on lactic acid bacteria growth. Analysis of organic (n = 15) and conventional (n = 15) farm milk using GC-MS revealed differences in fatty acid (FA) concentrations, mainly mono-, polyunsaturated fatty acids, and conjugated linoleic acid. Individual FA, such as stearic, linoleic, and oleic acids, were up to 33.6%, 31.0%, and 25.23% higher in conventional milk. Detection of the whey proteins using the enzyme-linked immunosorbent assay (ELISA) showed lysozyme content was up to 40.6% higher in conventional (22.04 µg L⁻¹) than in organic (15.68 µg L⁻¹) milk. Conversely, lactoferrin content was 20.4% higher in the organic (45.27 µg L⁻¹) than in conventional (36.04 µg L⁻¹). No difference in the content of immunoglobulin A was found. The higher concentrations of lysozyme, mono- and polyunsaturated fatty acids in conventional milk could enhance a higher inhibitory activity against lactic acid bacteria compared to organic milk.