In the present study, we investigated to what extent soybean was used in industrial and homemade sausage produced in Kosovo, as well as its potential impact on the fatty acid profile. In total, 63 samples, 42 industrial and 21 traditional sausages, were collected either from the market or the production site. All samples were tested by means of real-time PCR for the detection and quantification of soy content, as well as the GC-FID to determine the potential reflection in the fatty acid profile. The presence of soy DNA was detected in 54 out of 63 samples. In total, 41 out of 42 industrial sausage samples were positive for soy DNA, with an average ct value of 22.60 and a standard deviation (SD) of 4.28, whereas 13 out of 21 traditional sausage samples were positive for soy DNA, with a mean ct value of 23.36 and a standard deviation (SD) of 4.56. There was a statistically significant difference in means between industrial sausage and traditional sausage, with p ≤ 0.001 based on CT values (ANOVA test). We investigated the correlation between ct values in real-time PCR for soy DNA with each fatty acid content. There is a moderate correlation of soy DNA ct values with C16:0 palmitin (decrease), C18:0 stearic acid (decrease), C18:1 oleic acid (increase), and overall saturated fatty acids (decrease). With the exception of C14:0 Myristin, C18:1 oleic, and C20:0 Arachin acids and monosaturated fats, the ANOVA test reveals a significant difference in means between groups for the majority of the fatty acids between industrial sausages and traditional sausages. The current study demonstrates that the fatty acid composition of sausages is influenced by the amount of soy present in them. The extent to which other components affect the fatty acid profile is unknown. However, an increase in oleic acid and a decrease in stearic and overall saturated fatty acids are expected.