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Growing Coneflower From Seeds Dampen a Paper Towel Fold a paper towel in half. Sprinkle it with water until it's barely damp but not soggy. Treat the Seeds Sprinkle the coneflower seeds on one-half of the paper towel. Fold the towel in half so the seeds are between two layers of moist towel. Seal the towel in a plastic bag and keep it in the refrigerator for eight to 12 weeks. This cold treatment mimics winter conditions and helps the seeds break dormancy so they can germinate. Prep the Pots Fill 8-inch-deep seedling pots with moistened potting soil. Coneflowers need extra-deep pots because they develop very long taproots. Sow the Seeds Sow two coneflower seeds in each pot, covering them with only a thin sprinkling of soil, and allow the pots to drain. Cover the Pots Cover the pots with clear plastic to retain moisture and keep the pots in a warm room to germinate. Remove the Bag Remove the bag once the seeds sprout and provide the seedlings with full sunlight. Water the plants when the soil surface dries. Transplant the Seedlings Move the coneflowers outside once they produce their second set of true leaves and after average nighttime temperatures are above 55 degrees Fahrenheit. Transplant them to a full-sun, well-drained perennial bed. Water the Coneflowers Provide coneflowers with approximately 1 inch of water a week during the growing season. Apply up to 1 inch of compost around each plant in spring to replenish the nutrients in the soil.