Red clover (Trifolium pratense L.) is an important legume that is also known as a rich source of isoflavones, which are compounds with mild estrogenic activity. Therefore, this plant is often used as a raw material in the production of dietary supplements recommended in menopause. Many factors can influence isoflavone content, but those genetically related are considered to be the most important. Therefore, the aim of this study was to evaluate the phytochemical profile of different plant parts of 30 red clover genotypes grouped according to ploidy and country of seed origin by analyzing the content of dominant isoflavones, total phenolic content (TPC) and antioxidant activity. It was found that there are significant differences in the examined traits among plant parts. Red clover leaves had the highest total isoflavone content, with biochanin A as the dominant compound, while flower extracts had the highest TPC and antioxidant activity. Diploid and tetraploid genotypes were significantly different concerning the content of daidzein, genistein, formononetin and TPC with higher quantities in tetraploid samples. On the other hand, seed origin was not a useful separating factor for the analyzed samples. The results of this research indicate that ploidy, as a previously poorly studied factor, could influence isoflavone content in red clover.