How to harvest heirloom tomato seeds Follow these instructions for saving your own tomato seeds for next spring Harvesting heirloom tomato seeds Step 1Wash your heirloom tomatoes, then cut it in half across the middle (not the stem end). Gently squeeze tomato seeds and juice into a labeled glass or plastic container.Fill containers about half full, then set them out of direct sun in an area where you won't be bothered by the ripening odor or fruit flies.Full story: Why save tomato seeds from year to year? Pinterest Step 2 Allow the seed mixture to sit until the surface is partially covered with whitish mold (in three to five days). In warm climates, you may need to add a little water midway through the process to keep the seeds afloat. Scrape off the white mold with a spoon, being careful not to remove seeds. Step 3 Fill the container with water, then stir; the good seeds will sink to the bottom. Step 4 Pour off and discard floating seeds and pulp. Repeat until the good seeds are clean. Pour the cleaned seeds into a fine strainer; rinse and drain. Step 5 Sprinkle seeds onto a plate and allow them to dry for one to three days, depending on the weather. Keep them out of direct sun. To make sure they dry thoroughly and don't stick together, stir twice a day.Store dried seeds in a cool, dry, dark place in individually labeled airtight containers such as glass canning or baby food jars until planting time next spring.