Intensified use of fertilizers enhances crop yield; however, it can also make weed management more challenging. In addition to providing nutrients to crops, fertilizers also provide nutrients to weeds when they grow together with crops. All this leads to competition between crops and weeds, which is an important source of biotic stress. As a defense mechanism against biotic stress, plants accumulate polyphenolic compounds and increase antioxidant activity. This study aims to quantify the influence of organic and synthetic fertilizers on weed behavior and competitiveness in agroecosystems by evaluating total phenol content, polyphenolic acids (chlorogenic, ferulic, p-coumaric, and trans-cinnamic) content, and their antioxidative activity in weeds (Avena fatua and Abutilon theophrasti) and wheat and their rhizospheres across different cultivation systems (monoculture vs. competitive conditions). Our study showed that under competitive conditions, the use of fertilizers significantly increased the concentration of selected individual phenolic acids in all tested species (weeds and wheat) compared to monoculture. In addition, the level of antioxidant activity and total phenolic content in the weed leaves (Avena fatua and Abutilon teophrasti) was higher compared to the control after the application of all tested fertilizers when grown in competition with wheat (total phenolic content in Avena fatua: C vs. F1 p = 0.025 *, C vs. F3 p = 0.008 **; in Abutilon teophrasti: C vs. F2 p = 0.0000 **). The application of all tested fertilizers affected the increase in antioxidant activity in weed plants (p = 0.0000 ** in Avena fatua and in Abutilon teophrasti C vs. F1, p = 0.013 *, and C vs. F2, p = 0.0012 **). This shows that, in plants, response to stress levels not only total phenol, but also their antioxidative activity should be taken into consideration.