Artichoke herb is of great pharmaceutical importance, mainly due to the high content of phenolic compounds. This paper presents the effect of late nitrate (N) fertilization with mineral and organic N on the yield of air-dried herb, the total content of polyphenolic acids (TCQA), the polyphenolic profile as well as on the antioxidant activity (AA). These parameters were measured in organic (ORG) and conventional (CON) cropping systems. The principal outcomes revealed that the highest TCQA content was determined in the herbal extracts of ORG management treatments with late N fertilization of 20 kg ha−1. This result explained the highest AA content of the extract in the ABTS+ (2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid)), FRAP (ferric-reducing antioxidant power), and DPPH (2,2-diphenyl-1-picrylhydrazyl) assays. Late N fertilization increased the content of cynarin and ferulic acid in both systems. In addition, chlorogenic acid increased between 37% and 45% in the CON cropping systems depending on the fertilizer dose. In the same treatment, luteolin increased 39% compared to the control. Lastly, in the ORG management system, caffeic acid and apigenin content increased 10% and 30%, respectively. Both treatments showed high collinearity values, where ORG systems were related to ferulic acid and cynarin, and CON systems were associated with chlorogenic acid and AA potential (ABTS, DPPH, FRAP). To sum up, ORG cropping systems can obtain an acceptable yield size with a high-quality content of bioactive compounds, allowing a better understanding of the effect of N fertilization in ORG and CON cropping systems.