How to Start Seeds Indoors and Keep Them Alive!

Starting seeds indoors can be a challenge, but it is so rewarding. Instead of paying several dollars per plant from a nursery, you end up only spending pennies per plant by growing them yourself from seed. Starting your own seeds may seem intimidating, but I promise, anyone can do it.

I have a deep love for growing my own plants from seed. Since I discovered my love for gardening, I have personally started several hundred varieties of vegetables, herbs, flowers and fruits from seed and cutting propagation. It is a true passion of mine!

Learn the entire process for indoor seed starting success including: setting up your growing space, what supplies to purchase, when and how to plant, seedling care, common seed starting problems, hardening off and transplanting.

You can also save seeds from your own vegetable garden to start indoors or outdoors the following spring! To learn more, check out my E-book “Saving Vegetable Seeds – a quick start guide“.

Setting up your indoor growing space

The Set Up

We all dream of having a giant heated greenhouse filled with thriving seedlings, but the reality is, most of us don’t have space, money or time to build one. I have successfully started multiple flats of seedlings every spring inside my house, and you can too!

If possible, place your seedlings in a south facing window (if you’re in the northern hemisphere). East or west facing windows would be a second choice, but try to avoid a northern orientation. This will ensure the plants receive the most amount of sunlight possible. You will need to visit the plants daily, so be sure your set up is convenient.

Seedling window growing set up
My Hanging Window Shelf Set-up

Tall shelving is a space efficient way to fit many plants into a small window. I take a wire closet shelf and hang it from the curtain rod in my window (make sure it’s securely mounted) to give an extra level of seedling space. Below that, I have a piece of furniture that lines up perfectly with the height of my window sill for the heavier pots.

Greenhouse trays are great for allowing water to drain from pots without spilling onto the floor. Then you can switch from small seedling cell trays to larger pots as your plants grow while keeping the trays in place. Trays also make it convenient to carry multiple pots outside when hardening off. Humidity domes help retain moisture, heat and humidity while seeds are germinating and seedlings are small. There are different heights of humidity domes, the taller they are, the longer your plants can grow in them. Clear plastic bins are another sturdy option to use as a mini greenhouse for larger plants. Always have labels on hand for as many plants as you intend to grow.

Adding grow lights on a timer to help supplement light levels will also benefit your plants. If you see them leaning or reaching for light and becoming tall or leggy, then they are not getting enough light from the window alone. Grow lights can be suspended from the bottom of the shelves and mounted over the plants on the shelving. If you want to take the guess work out, you can purchase a ready to assemble shelf with grow lights like the one below.

Grow lights of tiered shelf
Grow lights on tiered shelf

Plan Ahead

Before you start popping those seeds into soil, take some time to plan out how many of each variety you will need. I always start more seeds than I plan on planting, just in case some of them don’t make it. Seedlings are fragile little things and a lot can go wrong, so it’s nice to have backups. If you end up with too many plants, sell some or give some away to friends.

Determine how you will layout your garden and how many of each plant variety will fit. Then start a few extra of each. If you are starting many different varieties of plants, it may be helpful to draw up a propagation tray diagram to make sure you have enough space for all the seedlings as they grow. Then plan a schedule for when each type of seed should be started (more on how to do that below).

Seed Selection

The variety of seeds you purchase can have a huge impact on your overall success. Make sure you read the descriptions carefully to determine if the plant grows well in your area or hardiness zone.

Now for a little plant genetics. You may see some seeds marked as heirloom. This means that their genetics have been preserved over the generations and their viable offspring are identical to the parent plant. Heirloom seeds today are the same as the varieties your great grandparents would have grown. They are open pollinated and their seeds can be saved for future seasons. I love the selection of heirloom seeds from Seeds Now, they have a huge variety of time-tested, heritage cultivars (plus I just love reading the plant origin stories!).

Some seed varieties have been bred to be resistant to certain diseases or pests. There are two ways in which this is done, cross-breeding plants or laboratory gene splicing. When two different varieties of the same species are intentionally crossed, they are referred to as hybrid. Cross-pollination can happen naturally, and even accidentally, when similar varieties of plants are near one another. The squash/melon family is notorious for cross-pollinating. Sometimes this produces desirable traits and a hardier plant, but seeds saved from hybrid plants will produce unreliable offspring that may not be true to type.

If you see a seed labeled GMO (genetically modified organism), this means that human science has changed the genome of the plant in a lab. Although there is much controversy over the safety of this practice to our health, it has helped commercially grown crops survive pests and diseases that would have otherwise wiped out much of our food supply along with farmer’s profits.

Organic is a term used often on seed packages. This simply means that the parent plant was grown without the use of chemical contaminants such as pesticides or fertilizer. Farms must be chemical free for 3 years to receive this label. Sellers can legally only use the term organic if their product has been certified by the US Department of Agriculture.

Choosing seeds for your garden

Should You Start Indoors or Direct Sow?

When your planting instructions say to direct sow a seed, this means you should plant it directly in the ground outside. Depending on the type of crop, the seeds can be sown before your last spring frost for cold hardy plants (onions, carrots, peas, potatoes, lettuce, radishes, etc) or after the danger of frost has passed for heat loving plants (melons, peppers, eggplant, tomatoes, squash, etc).

Some seeds have the option to be direct sown or started inside. This is where it can get tricky to decide what to do. If you live in a climate with longer winters and a shorter growing season, you will benefit from starting seeds indoors for heat loving plants when possible. Check the “days to maturity” for your crop variety and then compare this number to the average frost free days in your growing zone to determine if you will have enough time for the fruit or vegetable to ripen.

For example, where I live in Michigan, my last spring frost is approximately May 10th and my first fall frost is around October 4th. I usually play it safe and subtract a couple weeks since I have often seen frosts as late as May 30th. So my growing season is around 125 days, give or take.

So, if I wanted to grow a crop such as sweet potatoes, which can’t survive frost and need 90-170 days to mature, I would need to start them indoors. Tomatoes have 50-90 days to maturity, so they could be sown outside where I live. But since they can be harvested for a period of several months, I gain a lot more harvest time by starting them inside 6-8 weeks before my last spring frost.

There are also some plants (like radishes, carrots, squash and melons) that are sensitive to root disturbances from transplanting. They can be started indoors, but take extra care to be gentle with their root systems. When the small hairs on a plants root system are damaged, plants are unable to take in the water they need.

I know, it’s a lot to figure out. Here is a handy reference to help you determine which seeds to start indoors and which to start outdoors. Of course, you can grow any kind of seed indoors if you desire.

When to Plant What

Most seeds will come with planting instructions that tell you how many weeks before your last frost date to start them. To determine your last frost date, visit The Old Farmer’s Almanac. Then count backwards the number of weeks indicated for each plant.

If you need a little more help figuring out your planting schedule, try my Garden Design and Planning Tool. It come pre-formatted with each plant’s days to maturity, so you can schedule your planting dates without having to do all that research.

How to Plant Seeds

Start by filling your seed starting containers with a soil mix specifically formulated for starting seeds and press it down. Then completely soak the soil before you plant any seeds. Often, commercially made potting mix is sold completely dried out to reduce the weight for shipping. The first time it’s wet down, water runs all over the top before soaking in. If you put your seeds in before watering it, they could float around and end up settling and germinating where you didn’t intend them to.

Check the recommended seed planting depth for each seed you are planting. Generally, small seeds should be planted at a depth of 1/4 inch or less and larger seeds should be a bit deeper, anywhere from 1/2 inch to 2 inches. If seeds are planted too deep, they may sprout, only to die before they can reach the top of the soil. Seeds typically need to be planted at a depth 2-3 times their size.

A rule of thumb is to plant 2-3 seeds in each cell or pot to ensure you have a seedling germinate in each. Seeds that are older or have a lower germination rate (usually indicated on the seed packet) may end up needing more seeds per cell. You can always start more seeds in a week or two if you experience poor germination. Don’t forget to label your plants when you sow the seeds.

Seedling with roots, a stem and seed leaves


Seeds sit dormant while they are deprived of moisture and light. But when they have the correct combination of moisture, heat, oxygen and light, they will awaken to form tiny seedlings with roots, a stem and seed leaves. This process is called germination.

Pre-sprouting is a method used to germinate seeds before planting them in soil and often results in higher germination rates. There are several methods for pre-sprouting. One method is to soak seeds in a bowl of warm water for 12-24 hours, then rise once a day until they begin to sprout roots. Another way to sprout seeds is to lay them on a wet towel for several days to germinate. Once they have sprouted, plant the seeds in soil and water well. Pre-sprouting is useful for testing to see if old seeds are still viable. It works best with larger seeds because they are easier to handle and plant after germination. Always be delicate when planting.

Watercress Seeds Sprouting

There are different requirements for germination that vary from one type of plant to another. Lavender seeds, for example, needs to go through 6 weeks of cold, wet conditions to germinate (a process called cold stratification). Some seeds need a period of light or darkness to wake them up, while others need warm or cold temperatures. Research the seeds you are planting to see if they have any special requirements before planting. A heated mat placed under seedling trays or pots can speed the germination process and growth for heat loving plants.

Failure to germinate is a common seed starting issue and can be the result of seeds that are too old or seeds that have been improperly stored. Incorrect seed depth and temperature can also cause lower germination rates.

When seedlings first emerge from their seed coat, they have two seed leaves. After a few days to a week, they continue to grow to form their first set of true leaves. Plants are not hearty enough to be re-potted until they have their true leaves.

Seedlings with their seed coat still attached to their seed leaves


The one thing I can’t stress enough – don’t wait too long to repot! It’s a great space saver to use tiny cell trays to start seeds, but the seedlings must be re-potted or “potted up” into a larger size cell tray or pot when they reach 2-3” tall or have 2 sets of true leaves. They may look small, but their root systems can be deceivingly large. The growing roots need space, nutrients, and a larger water source, which are provided by a greater volume of soil. Depriving a small plant of these resources will result in a wilted plant. A wilted seedling whose conditions don’t improve can die with 24-48 hours. So please, don’t wait to repot a seedling that is showing signs of decline.

Repot seedlings to give them the space and nutrients they need.

Choose a pot that is at least double the size of your plant’s current container. Water the seedlings before transferring them over. Fill the bottom of the new pot with soil and water it before adding the seedling. Next, tip the seedling pot upside down into your opposite hand and let the plant’s stem hang between your fingers. Gently squeeze the pot to loosen the soil block and roots from the container and catch it with your other hand. Don’t ever tug on the stem of a plant when re-potting.

Place the seedling into the center of its new container and fill around it with soil. Some plants, such as peppers and tomatoes, will grow a stronger root system if they are transplanted deeper into the soil. However, most plants will not tolerate this, so try to match the soil level of the seedling when re-potting.

Seedling Care and Troubleshooting

Seedlings need a lot of care and attention. Negligence can leave you with a lot of disappointment, as seedling issues can arise out of nowhere and small plants can fail if their needs are not addressed within hours. Plan to check on your seedlings at least once per day to ensure all of the following needs are being met.

Sometimes, no matter how hard we try, things just go wrong for those little seedlings. If your plants are truly suffering, there is a strong chance that they won’t bounce back from their ailment. Sometimes the best thing to do is remove them and start over with new seeds.

Thin Your Seedlings

Remove any extra seedlings that may have emerged as soon as possible so that there is only one seedling per cell or pot. Always leave the strongest looking seedling when thinning. To avoid disturbing fragile root systems, cut these excess seedlings with a pair of scissors. Why should you thin? Because seedlings require a lot of nutrients and space to develop into hearty specimens at maturity. Having more than one seedling sharing resources will only result in scrawny, deprived and stunted plants.

Result of thinning to one seedling per cell


It can be difficult to maintain proper soil moisture in small containers. To gauge moisture levels, press your finger an inch into the soil. If it feels dry, it’s time to water. A soil meter can also give you accurate feedback on your soil’s water content. You will find advice out there to keep seedlings consistently moist, but this is an easy way to over-water. While you don’t want your seedlings to go too long without water, you don’t want them to be constantly soggy either. It is a delicate balance.

Plants that are suffering from over-watering May show signs of stunted growth, yellowing leaves or mold/algae growth. Plants essentially drown because they are not able to take in oxygen through their root systems. On the other hand, under-watering can cause wilting, stunted growth or curled dry brown leaf tips. If your plants show signs of over or under-watering and do not improve with a change in care, they may instead be suffering from a disease.

For small seedlings, I prefer a fine mist spray bottle. For plants in larger pots, an indoor watering can is a much quicker method. Always water the soil, not the foliage. Aim for a slow flow when watering so that water is absorbed evenly. Watering too quickly can cause dry pockets in larger pots where fast moving water runs around. Be sure to choose nursery pots with drainage holes to avoid water logged plants.


Seeds prefer warm conditions to germinate (although temperature preferences vary from species to species). Heat loving plants can germinate and grow faster with the use of a seedling heat mat. Since most seedlings enjoy temperatures of 70-80 degrees Fahrenheit, which unheated outdoor greenhouses often can’t achieve, an indoor growing space works well.

If plants get too hot however, you will see signs of heat stress which causes water loss through the plants leaves (called transpiring). This causes the plant to wilt and should be remedied immediately by lowering the temperature and increasing air flow around the plant.

Humidity and Air Circulation

Seedlings need humidity of at least 60%, but preferably higher until their root systems become more developed. Using a humidity dome or mini greenhouse can help keep humidity levels much higher than that of the surrounding atmosphere. Just make sure there is a way to allow ventilation since overly humid conditions can cause mold or bacteria to grow which can cause root rot or fungal diseases.

Plants should be allowed fresh air circulation to avoid wilting. The use of a fan is helpful to keep air flowing and it helps strengthen seedlings that will need to withstand strong wind and storms when they are moved to the outside world.


Plants need a certain number of hours of sunlight each day to thrive. If your growing space doesn’t receive at least 12 hours of direct sunlight a day, you may need to supplement light levels with grow lights. Leggy or leaning seedlings are a clear sign that light levels are too low. Leaf yellowing is another sign that your plant may not be getting enough light, although lack of water can also cause this.

If you can’t find any windows that will work for growing seedlings, a grow tent with lights can be used in any space. The reflective material on the inside helps bounce light around so that plants catch every ray. They also help keep humidity levels up through condensation.

Pests and Diseases

Sometimes pests can find their way indoors. Some common indoor pests are gnats, mites, aphids, leafminers, mealybugs, and springtails, amongst others. To get rid of indoor pests, you can vacuum them up and then spray plants with a mixture of 1tsp dish soap to 1 gallon of water.

Seedlings can be affected by a wide range of diseases which are caused by bacteria, viruses and fungi within the soil. Under warm moist conditions, these microorganisms thrive and deprive plants of nutrients. Dampening off is one of the most common seedling diseases and is caused by a fungus in soil. If this happens, remove the diseased or dead seedlings immediately to keep it from spreading.

Prevent seedling disease by sterilizing all tools, containers and equipment and don’t reuse soil where diseased plants have grown before. You can also sterilize seeds before germination by soaking them for 5 minutes in a solution of 1 TBS cider vinegar and 1 Cup of water. Once seedling disease takes hold, it is nearly impossible to save the plant. If you want to attempt to revive diseased seedlings, give them increased air circulation and allow the soil to dry out slightly in between waterings. You can also treat with a natural fungicide such as chamomile or cinnamon.

Hardening Off

Seedlings that are kept in a controlled environment like a greenhouse or indoor window sill are susceptible to shock from exposure to the elements. Outdoor conditions can be quite harsh, from strong winds to intense rain to the scorching sun. Seeds that begin life outside are made strong by these conditions and have a much better chance of surviving rough weather. But tender seedlings grown indoors do not receive this “toughening up” that Mother Nature provides. So it’s up to you, the gardener, to strengthen your plants and prepare them for the outside environment.

When your seedlings are 1-2 weeks away from their transplanting date (or 1-2 weeks before your last spring frost), start to condition them to the outdoors. Place your pots in a sheltered area outside for 1-2 hours the first day, then gradually increase their time outside over the course of a week or two. Don’t keep them outdoors if temperatures are below 50 or during a storm. Always bring seedlings inside at night to protect them from sudden drops in temperature.


Prep your garden beds well before your plants are ready for transplanting by removing any weeds, amending the soil, and adding any trellises or cages you plan on using. You want to disturb the soil as little as possible after transplanting.

When plants have been properly hardened off, they are ready to go out into the garden. Seedlings often experience root damage during transplanting, which makes it harder for them to take up water. This can cause wilting and can be remedied by keeping the seedling well watered until it’s root system strengthens from the shock. Adding sprinklers, a drip irrigation system or olla pots can help reduce the amount of time you spend watering and conserve water.

Transplanting is a wonderful opportunity to add nutrients and enrich the soil around the planting site. Eggshells can be added for calcium, coffee grounds for nitrogen, epsom salt for magnesium, manure for phosphorus, or you can add a balanced organic fertilizer or compost. To suppress weeds and retain moisture mulch around plants with wood chips, dead leaves, straw or pine needles.

What if Frost Comes Late?

Oh no, those precious seedlings you worked on for weeks are suddenly in danger of being killed by a late frost. Don’t panic, there are measures you can take to protect them.

An insulated tunnel, row cover or even blankets can offer protection from cold weather and frost. You can also use a portable garden cloche to create a mini greenhouse effect around tender plants. Another option is to surround plants with large jugs of water to act as a thermal mass. (They absorb heat during the day and emit it when temperatures drop at night.)


Have you tried everything and still can’t figure out what’s going wrong with your seedlings? Leave a comment or send me a message and I would be happy to help you identify problems and give you gardening advice. There are also some great forums or Facebook groups out there full of fellow gardeners who would love to offer solutions and ideas. Good luck and never give up on your seed starting dreams. Failures are just lessons on what doesn’t work. You can do it!

Learn the process for indoor seed starting success
How and why to harden off your seedlings

8 thoughts on “How to Start Seeds Indoors and Keep Them Alive!”

    1. Celery is by far one of the most difficult plants to grow (at least in my experience). Much trial and error there. The reason your plants are bitter is likely that they are overly mature (just like lettuce becomes bitter). It may also be poor growing conditions. I don’t have space here because it would take an entire blog post to answer this. But my advice is: start from seed, water very regularly, be very careful to avoid root disturbance and plant in full sun. There are different varieties, but many do well with a trenching or mounding method similar to how you grow potatoes. Plant the celery in a trench and hill soil up around the stalks as they grow taller. I hope that helps! Good luck this season.

  1. This was such a thorough “getting started” article! Thank you for writing this, I learned so much!

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