Arnica montana L. is one of Europe’s endemic endangered medicinal plants, with diverse biological activities commonly used in medicine, pharmacy, and cosmetics. Its flower heads are a rich source of raw material, with antibacterial, antifungal, antiseptic, anti-inflammatory, antiradical, antioxidant, and antitumor properties. The objective of the present study was (i) to characterize the chemical composition of flower heads of A. montana plants cultivated under nitrogen fertilization, (ii) to identify the impact of the nitrogen fertilization and extraction method (water, ethanol) on the antioxidant activity of extracts, and (iii) to determine the role of different nitrogen doses applied during plant cultivation and different extraction methods in the anticancer activity of the extracts through analysis of apoptosis and autophagy induction in HT29, HeLa, and SW620 cell lines. The present study shows that nitrogen is a crucial determinant of the chemical composition of arnica flower heads and the antioxidant and anticancer activity of the analyzed extracts. Nitrogen fertilization can modify the composition of pharmacologically active substances (sesquiterpene lactones, flavonoids, essential oil) in Arnicae flos. The content of sesquiterpene lactones, flavonoids, and essential oil increased with the increase in the nitrogen doses to 60 kg N ha−1 by 0.66%, 1.45%, and 0.27%, respectively. A further increase in the nitrogen dose resulted in a decrease in the content of the analyzed secondary metabolites. Varied levels of nitrogen application can be regarded as a relevant way to modify the chemical composition of arnica flower heads and to increase the anticancer activity, which was confirmed by the increase in the level of apoptosis with the increase in fertilization to a level of 60 kg N ha−1. The fertilization of arnica plants with low doses of nitrogen (30 and 60 kg N ha−1) significantly increased the LOX inhibition ability of the ethanol extracts. The present study is the first report on the anticancer activity of A. montana water extracts, with emphasis on the role of water as a solvent. In further studies of factors modifying the quality of Arnicae flos, attention should be paid to the simultaneous use of nitrogen and other microelements to achieve synergistic results and to the possibility of a more frequent use of water as a solvent in studies on the biological activity of A. montana extracts.