The effects of Perilla frutescens pollination on the content of seed antioxidants were analysed by agronomical and pollination trials, comparing seeds produced from bagged plants in 2013 (A) to prevent access to pollinating insects, and seeds from open-pollinated plants in 2013 (B) and 2015 (C). The seeds of open-pollinated plants were significantly more numerous and heavier than those of self-pollinated plants. 1H NMR seed analysis showed a higher presence of phenolic compounds in open-pollinated seeds, mainly rosmarinic acid and flavonoids, apigenin and luteolin. Flavonoids were present in the glucosylated form in seeds (A) and (C), and in the aglycone form in seeds from (B) plants. Saturated and unsaturated fatty acids (palmitic, linoleic and linolenic) were more abundant in seeds from self-pollinated flowers. Pollination performed almost exclusively by the honeybee notably increased the antioxidant content in perilla seeds and gave rise to a reduction in the fatty acid content.