Best Method for Starting Seeds Indoors

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Robert Pavlis

There are several different methods for starting seeds indoors that work well for vegetable seeds and flower seeds. In this post I will review the various seed starting methods and help guide you in selecting the right method for your situation.

None of the seed starting methods are right or wrong – they all work and produce results. Each method is the best when it is matched to the right type of seed and the correct home environment. Learn about the best germination method for both vegetable seeds and flower seeds.

Best method for Starting Seeds Indoors
Starting Seeds Indoors

Starting Seeds Indoors

There are three basic ways to start seed indoors; in pots or containers, the paper towel or baggy method and winter sowing. The last one is not really a form of starting seeds indoors, but it is a good alternative for home owners.

Within each seed starting method there are a number of variations.

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Light Source

Once seeds germinate, they need light to grow and a good light source is the most limiting factor for home owners growing indoors.

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You can grow seeds near a window, but due to space this usually limits the number of seed types you can grow. It is however inexpensive and requires no special equipment.

Seeds grow well under lights since they don’t need as much light as adult plants. You can use florescent lights which have been the standard for many years. They are easy to use, relatively inexpensive, and easy to install. More recently people have started using the new LED version of florescent fixtures which now cost about the same as a florescent fixture. Early reports show that they will work just as well, and they use even less electricity.

If you don’t have a good light source you can still start seeds with the winter sowing method.

I plan to have a more detailed post about lights in the future but for now you can see several videos about light systems here Great Gardening Videos Playlist.

Cold Stratification

Stratification is a process of pre-treating seeds to help them germinate. The details are fully explained in What is Seed Stratification?

Starting Seeds In Pots and Containers

Using this method you take a pot or container of some type and fill it with soil. Plant the seeds in the pot, water it, and wait until the seeds germinate. This is the traditional method for starting seed, and it works very well for all types of seed including vegetables, flowers and trees.


  1. Simple. You can use plant pots or even recycle old containers, as long as you punch some bottom holes into the latter. You can use garden soil but buying seedling mix is a better option.
  2. Once seed germinates it can grow right in the same pot until it is ready for the garden.
  3. Method works well for small and large quantities of seed.
  4. Works well for indoor plants and garden plants.


  1. You can’t see the seed germinate. If nothing grows, it is difficult to figure out why. Was there no germination – the seed might have been dead? Did the seed germinate but then die – maybe you have a fungus or pH problem?
  2. Cold stratification is difficult in pots unless you have a dedicated fridge for plants, or a cold fruit cellar.
  3. Seeds that take a long time to germinate need to stay in the pot a long time. This becomes a lot of work in summer when the pots dry out quickly and need to be watered every day.
  4. A light source is needed to grow the seedlings. Both artificial lights and windows provide a very low level of light compared to the sun. This results in etiolated seedlings (ie tall and skinny).

Starting Seeds in Jiffy Pellets

Jiffy pellets are special disks of peat moss that expand in water. A plastic mesh holds the peat into the form of a pot. I have written about this product before. In summary – don’t use it. For a more detailed review have a look at Jiffy Peat Pellets – Not Good For The Environment?

Starting Seeds in Paper Towels or Baggies

The paper towel and baggy method are very similar and are used to germinate seeds. To understand the difference between the paper towel method and the baggy method have a look at this video:

YouTube video

If you can’t see the above video try this link:

In this method, seeds are put on paper towels, and kept in a plastic bag so that they remain moist. When the seed germinates, they are transferred to pots or containers to grow.


  1. You can see the germination process. Not only is this exciting, but it can tell you a lot about your seed. If you never see the root in the baggy you know that the seed is either not viable, or the pre-treatment was not the right one. If it germinates ie produces a root, then it is viable. If subsequently, the seedling dies it is not a germination problem.
  2. A lot of seed can be germinated in a small space using this method. You can hold 100 baggies of different seed in one hand – try doing that with 100 pots. Granted, if you are successful with all 100 seeds, they do need to go into pots at some point.
  3. Seed that takes a long time to germinate requires little care since the seed stays moist in the baggy.
  4. Stratification procedures are easy to carry out since the bags take up so little room in a fridge.
  5. Maximum use of seed. Since you can see which seed germinates, you need fewer seeds. In the potted method most people plant excess seed and weed out the extra. With this method you can put each seed into its own pot. This can be a real benefit for rare or expensive seed of limited quantity.


  1. Requires an extra step. You have to put seed into baggies, and then you still need to pot them up. But you only pot up the ones that germinate.
  2. Extremely small seed can be difficult to handle. The video below shows you how to handle small seed using the baggy method.
  3. Baggies need to be examined more frequently for germinating seed than pots.
  4. No special lights are needed for germination, but once they are potted up they need the same light as any growing seedling.


YouTube video

If you can’t run the above video use this link:

Vermiculite and Baggies

This is a variation of the above baggy method. Instead of using a paper towel in the baggy, it is filled with vermiculite that has been barely moistened. Some people also use peat moss, or seed starting soil instead of the vermiculite.

This works in much the same way as the paper towel – it keeps seed moist.

Vermiculite has the advantage that growing roots and shoots do better in vermiculite than in the small air space between the paper towel and the plastic. This means you don’t have to look at your seed quite as often since they can grow for days or even weeks in the vermiculite.

The down side to this method is that you can’t see smaller seed as easily. I find vermiculite works great for large and very large seed, but I don’t like it as much for smaller seed because I can’t see them.

Best method for starting seeds - in vermiculite or soil
Best method for starting seeds – in vermiculite or soil

Seed Starting With Winter Sowing

The word ‘winter’ in ‘winter sewing’ refers to the fact that seed is germinated and grown outside in winter. Seeds are planted in containers that will act like little greenhouses. After planting, the containers are set outside, and left until plants are ready to be transferred to the garden.


  1. Minimum care. Once the seeds are planted, and the containers are outside, there is virtually no maintenance of the containers. Later in spring you might need to water a bit.
  2. No light source is required. The light source in this case is the sun which gives lots of light for free.
  3. Seedlings are short and tough. They are grown in cooler conditions with lots of light. They are much stronger than seedlings grown indoors.
  4. Stratification is not needed since the seeds go through a natural stratification process during the winter and spring periods.
  5.  Gardeners routinely use garden soil, which is less expensive than bought seedling soil.


  1. The method is not suitable for seed that can’t take frost. Some seed is damaged if it is frozen,and this method will go through a frost period. It is not suitable for some tropical plants and most indoor plants.
  2. You can’t see the seed germinate. If nothing grows it is difficult to figure out why.
  3. Less suitable for seed that needs a warm cycle before a cold cycle. The baggy method could be used to provide the warm cycle, followed by winter sowing.
  4. Anything that does not germinate by spring needs to be maintained and watered all summer, or discarded.
  5. There is no control over temperatures. Since you can’t control temperatures easily, it is difficult to do things like grow large tomato seedlings. If this is your goal it is better to start them inside where it is warm.


The following video will show you how to prepare containers for winter sowing.

YouTube video

If you can’t see the above video, use this link:

Which Seed Germination Method Is Best?

The best method is the one that meets your specific needs. Winter sowing is easy for most home owners and works with many of the more common perennial flower seeds as well as most annuals. It is also a good choice if you don’t have lights.

If you have indoor lights, the paper towel – baggy method works for a very wide range of seeds. I use the baggy method the most.

Very small seed is more easily done by seeding directly in pots or with winter sowing.

Seed that is easy and quick to germinate, like most vegetables, are easily done in pots.

Each method has advantages. Give them all a try so that you better understand them. Over time you will gravitate to the one that is best for you and your seed.


  1. Photo Credit: Nikos
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Robert Pavlis

I have been gardening my whole life and have a science background. Besides writing and speaking about gardening, I own and operate a 6 acre private garden called Aspen Grove Gardens which now has over 3,000 perennials, grasses, shrubs and trees. Yes--I am a plantaholic!

25 thoughts on “Best Method for Starting Seeds Indoors”

  1. Love the tip about turning the baggies seed-side down. I’ve lost many trying to get the roots out of the paper towels. I also like your winter sowng method. Will try that this year.

  2. Robert hi 👋🏾, when the seed germinates which way into the soil should it go, the sprout down or just lay it on the soil and sprinkle with more soil please, thank you

    • Yes – thin paper towel might work for some seeds. The one I use is too thick. I do sometimes cut the towel into small pieces and then plant.

  3. Can you list plants that need a warm and then cool cycle? I wonder if keeping those seedlings inside and then putting them out for winter sowing would be beneficial.

  4. I live in middle Georgia and am wondering how soon I could start my seed with the overwintering method? What’s the ideal outdoor temperature to start? (It stays warm here until late September/ early October)

    • If you are talking about winter sowing, you can start them any time. The point is to expose them to natural environmental conditions. In most cases I would do it around January 1.


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