Pros and Cons of Fermenting Seeds Before Storage

Most guides to saving seeds from tomatoes, cucumbers, and melons recommend fermenting the seeds before storing them. However, a short perusal of the directions for this procedure is enough to convince anyone that a fermented seed culture is a nasty, smelly mess. So is it really worthwhile? Or is there a better way?

Interestingly, some gardeners don’t ferment their seeds, but simply clean them up with a paper towel. These people suggest that fermenting takes more time and effort than is really necessary. On the other hand, advocates of fermentation insist that the process is essential for ensuring the best results.

So what’s the answer? Let’s find out.


  • Nature’s way. Yes, it’s true. Seeds from certain plants are cleaned by fermentation in nature. Just leave a tomato on the plant to ripen, rot, and fall, and you’ll see it in action. Fermenting seeds mimics the natural process.
  • Enhanced germination. Wet seeds that are embedded in soft fruit crops are often encased in protective gel coatings that keep them from sprouting while still on the plant. Fermentation ensures the removal of the gel, thus guaranteeing good germination rates.
  • Disease prevention. Some plants carry diseases that can be passed on to their seeds and then on to the new crop. During the fermentation process, yeast and beneficial bacteria destroy any diseases that might be lurking on the outside of the seed coat.
  • Bulk benefits. While fermentation may sound complicated to someone with just a few seeds to save, it is actually the easiest and most efficient way to save seeds from a large quantity of tomatoes or other fruits. More seeds means more scrubbing time and effort if you use the paper towel method; on the other hand, the size of a batch of seeds has little effect on fermentation, rinsing, and air-drying time by comparison.
  • Garden etiquette. If you share and trade seeds, you will make them more acceptable to other gardeners by fermenting them. Many gardeners are careful to avoid introducing outside diseases to their gardens, and fermentation will set their minds at ease even if you know that your plants are healthy.


  • Complexity. Fermenting seeds can be difficult even for the experts sometimes. There are many variables which affect the fermentation process, and the project will take close monitoring for best results. Then comes the lengthy washing process and the tricky task of drying the seeds.
  • Odor. Fermenting seeds are notorious for their smell. This is definitely not an indoor project, yet keep in mind that the mixture still has to be kept in a safe place.
  • Drying difficulties. Once the seeds have been fermented and rinsed, they must be dried. For some, this is the tricky part. Drying must take place quickly, or the seeds will absorb moisture and not keep well. On the other hand, they must be dried at cool temperatures, or some of the seeds will be injured or even killed. Seeds stay comparatively dry using the paper towel method.
  • Extra effort. For quite a few gardeners, the paper towel cleaning method works just as well. Why go to needless trouble?


Perhaps the answer to the question of whether fermentation is worthwhile depends on scale. A backyard gardener saving a few seeds for personal use can simply scrub them off with a paper towel and move on without any further hassle. On the other hand, someone growing more seeds, perhaps with plans to trade or sell them to preserve the variety, will want to go the extra mile and ferment them before storage. This person will have to take particular pains to ensure that all of the gel coating is removed from the seeds for both proper storage and good germination, and the paper towel will make slow work of it.

The good news is that gardeners have two equally viable options to choose from when saving seeds. Not everyone has to deal with the messy fermentation process, while those who want to ensure good germination rates and healthy seedlings have a reliable method at hand.

Helpful Resource


Our own online guide to raising vegetables offers tips on saving seeds, including step-by-step directions for fermenting cucumber and tomato seeds.

The Family Garden Journal