Troubleshooting Common Indoor Seed Starting Challenges: Overcoming Obstacles for Success (2024)

Navigate the common pitfalls of indoor seed starting with this troubleshooting guide, identifying and resolving issues for thriving seedlings.

If you’ve never started a garden from seed before, it is truly amazing how a tiny little seed can produce something beautiful or edible. I’ve been starting seeds indoors for a few years now and will share the best process from seed to flower (or vegetable if you want to grow them too).

But the best part?

You don’t need a greenhouse to start seeds indoors.

Whether you want to grow flowers, herbs, or vegetables, learn how to start seeds indoors without a greenhouse this winter. This post shares a comprehensive seed starting guide that covers the common pitfalls we meet when germinating seeds.

Are you ready to grow an amazing, bountiful garden this year?

Let’s go!

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9 Benefits of Starting Seed Indoors

While you can always shop your local nursery for plants and flowers, planting seeds indoors is a rewarding experience with lots of benefits for the home gardener.

For starters:

1. Better control over growing conditions (light, temperature, moisture)
2. Early start to the growing season
3. Protection from harsh weather
4. Reduced risk of disease and pests
5. Ability to grow rare or specialty plants
6. More efficient use of garden space
7. Budget-friendy way to grow plants
8. It’s a rewarding experience
9. Helps beat the winter blahs

Troubleshooting Common Indoor Seed Starting Challenges for Success

Before we get started, keep in mind that while there is a science involved with planting seeds indoors, it is SUPER EASY to do.

Read through this overview to get an idea of what you’ll need to do before getting started so you are ready to go when it is time to sow seeds.

Obstacle #1: Starting Seed Indoors When You Don’t Have a Greenhouse

I used to be under the mistaken impression that I could not successfully grow seeds indoors without a greenhouse. And that can not be further from the truth!

You absolutely DO NOT NEED A GREENHOUSE but you do need the right equipment. Regardless of the types of seeds you wish to grow, having the proper equipment is paramount to success with indoor seed starting. With the proper seed starting supplies, you can germinate seeds indoors anywhere you want.

As an aside, while this post focuses more on growing flowers, you can start any type of seed indoors using this process.

Why You Need the Right Equipment for Seed Growing:

While I have started plants from seed before with some success, it was pretty ho-hum before I started using grow lights.

Some plants started easily, while others were epic failures. Part of the problem was that I started seeds in front of my south-facing windows and there wasn’t much room to grow stuff there.

The windows were not very large so my seed-starting set-up sucked up a lot of my living space. And seedlings were not receiving an adequate amount of light to grow properly.

So it was a bit of a struggle to do it there.

And then the voice in my head took over. Telling me that I needed a greenhouse to be more successful.

And that couldn’t be further from the truth!

Change Your Mindset and You’ll Change Your Life

So if I want to expand my gardens to include more flowers that can be grown for cutting, I had to get that mindset. Because those flowers were not readily available at the nursery. Get the negative thoughts out of my head, get the proper equipment, and start them from seed.

Since I don’t have a greenhouse and can’t do them on a large scale in my living room, I started seeds in my basem*nt in my former home and the sunroom in my new home using the right equipment.

The first year I did this in the basem*nt and it was a great spot to start seeds because I had plenty of space to grow lots of plants and they grew much better using the proper equipment.

I mean, I started 1400 flowers in my basem*nt! It was pretty incredible and I was amazed at how much easier it was to use grow lights.

So the short of it is, yes you can germinate seeds in front of a sunny window, but if you truly want success with it, get the grow lights.

Obstacle #2: Finding the Right Location for Starting Seeds Indoors

If you are like me and do not have a greenhouse, find a spot in your home where you can sow seeds and place a growing system with lights. This could be in the same area or different locations depending on what you have access to.

Your seed starting station does not have to take up a lot of space, particularly if you use a shelf-type system.

Measure your garden space so you know how much of a DIY growing system you’ll need or purchase one that is ready-made. These measurements will help determine the size of your growing system, as well as the amount of seed trays you can fit.

Obstacle #3: Shopping for High-Quality Seeds

The better the quality of seeds you buy, the higher the success rate you’ll find with seed germination. How seeds are harvested and maintained in warehouses, shipping, etc. impacts the quality of seeds you want to grow. So it is very important to buy high-quality seeds.

While you can purchase seeds locally from nurseries, I like to purchase from quality growers online in December and January. Because there are far more varieties you’ll find online from high-quality growers than you’ll find in the store.

That doesn’t mean you shouldn’t purchase seeds from the store, but I’d be hesitant to purchase ones from big box stores and would opt for your seeds from your local garden nursery instead. Big box stores are great for many things, but I haven’t found their seeds to be high quality.

Now that does not mean you won’t find success with them, but the seeds may be dryer, and germination rates will likely be less high.

My favorite seed sources include:

• Floret Flower Farm
• Johnny’s Select Seeds
• Renee’s Garden

Since most online seed sales start in early January, I do my research beforehand, save a wishlist on their site, and then shop when their sales go live.

You’ll still find seeds online after December and January, but there may not be as many options or varieties to choose from.

Keep in mind, that some flowers and vegetables might need to be sowed sooner than later, so you will want to get your seeds early.

Obstacle #4: The Cost of Indoor Seed Starting Supplies

Depending on how many seeds you want to start indoors, the cost of seed starting supplies can add up. From the initial cost of your seed starting system to the soil, trays, etc. you’ll need to do yearly, the cost can outweigh the benefit if you are on a strict budget.

But all is not lost. Because you can get by with a few basic supplies and coming up with a DIY seed starting system. Choose reusable supplies that you can clean and use yearly, instead of one-and-done type supplies that you’d have to repurchase yearly.

We will cover more about my DIY seed starting system and supplies in the next post of this Grow With Me series, but in general, here is what you need for indoor seed starting.

• Seeds
• Vermiculite
• Seed Starting Potting Soil
• Seed Trays
• Bottom or Drainage Trays
• Clear Dome Lids
• Grow Lights
• Table or Shelf System for Seedlings
• Heat Mat
• Plant Labels
• Oscillating Fan
• Programmable Timer

Since I have a lot of space in my basem*nt and sunroom, I work with four-foot grow light systems on tiered wired shelves as my indoor seed starting setup.

But there are smaller options available so design a system that works best for you and the space you have.

Pro-Tip: When reusing seed starting supplies, it is essential to clean them really well with a 1:10 ratio of chlorine bleach to the water to sanitize and kill any pests or diseases lingering behind. This is actually a good practice for any pots or containers that you re-use for any type of plant.

Designing a DIY Seed Starting System to Keep Costs Down

There are tiered systems available like these from Gardener’s Supply. And I love when everything comes together like this. Plus, it’s easy to use and move around. But they can get pricey for how much growing space you get. And if you want to grow a lot like me, this would seriously bust the budget.

My husband wanted us to piece something together ourselves and make something similar to a pre-made tiered system like this one. That’s how we came up with our DIY seed starting system, and it works well and have been using it for several years.

So there’s no right or wrong way to set up your system as long as you have a way to hang grow lights above seeds and have the ability to adjust the height.

Obstacle #5: You Didn’t Plan When to Plant Seeds Chart

While gathering seed starting supplies, chart the timing and needs for each seed packet. Because when to plant seeds for spring is something you need to know before you start sowing.

It’s much easier to figure out how many supplies you’ll need after writing it all down. So read each seed packet and calendar their seed start dates together with plant requirements. And when you are organizing the seed start schedule, it’s important to know when your last frost date is.

In New Jersey, my last frost date is typically around or just after Mother’s Day, but in the last few years, it’s been stretched to mid-May. I still tend to plant tenders around Mother’s Day anyway, but watch the weather like a hawk and am prepared to cover anything that is susceptible to frost.

With the last frost date in hand, look through each seed packet. Write down the flower, variety, date of maturity, when it should be sowed, seed starting dates, overall size, and color.

When mine was all written down, I added it to a spreadsheet to organize the information better. Not only does this make planning the garden easier, but it helps hone my seed starting supply list too.

And you can even add a notes column so you can jot down any growing notes of what you learned during the season. Like did this variety need staking? Was it more susceptible to a resident rabbit? Did it germinate with ease?

Obstacle #6: Sowing Seeds and You Get Little Germination

There are several reasons why seeds might fail to germinate when started indoors. Understanding these factors can help troubleshoot and improve the success rate of seed starting.

Here’s what you need to know about growing seeds indoors and what can affect germination.

1. Incorrect Temperature

Too Cold: Some seeds require specific temperatures to germinate. If the environment is too cold, seeds may remain dormant or germinate very slowly. Ensuring the right temperature for each seed variety is crucial. Heat mats work well with helping seeds that need more heat to germinate. Read the seed packets well to discern whether or not the seeds you are growing require heat for better germination.

Too Hot: Conversely, excessive heat can also hinder germination. It can dry out the soil or cause the seeds to rot before they sprout.

2. Improper Moisture Levels

It’s a good idea to start with premoistened soil when you sow your seeds and bottom water your seedlings so you don’t damage tender seedlings from above.

Overwatering: Keeping the soil excessively wet can lead to seed rot or fungal growth, preventing successful germination. Seeds need moisture, but they also need oxygen, so soggy soil can suffocate them.

Underwatering: Conversely, if the soil becomes too dry, seeds won’t have the necessary moisture to begin the germination process.

3. Poor Seed Quality

Old or Low-Quality Seeds: Seeds lose viability over time, and if they are past their prime or were not stored properly, their ability to germinate diminishes. This is why it is so important to purchase high-quality seeds before starting. You’ll save yourself a lot of heartache later.

4. Incorrect Planting Depth

Seeds need to be planted at the correct depth to germinate successfully. If planted too deep or too shallow, they might struggle to push through the soil or receive inadequate access to light and moisture. Read the seed packet directions and follow the grower’s recommendations for planting depth.

5. Lack of Light

While some seeds germinate in darkness, many require adequate light to start the germination process. Insufficient light can lead to weak, spindly seedlings or inhibit germination altogether. When starting seed indoors, grow lights are essential. If there’s one thing you need for success, don’t skimp on the lighting.

6. Poor Soil or Seed Starting Medium

Using soil that’s too compacted, lacking nutrients, or contaminated can impede germination. A quality seed starting mix with good aeration and drainage is essential for healthy seedling growth.

7. Inadequate Air Circulation

Stagnant air around seeds can encourage the growth of mold or fungi, affecting germination. Adequate air circulation helps maintain a healthy environment for seedlings. Use an oscillating fan to improve air circulation in the room where you are germinating seeds.

8. Incorrect pH Levels

Seeds have specific pH preferences for germination. Soil that’s too acidic or alkaline can inhibit the process. Always start with a good seed-starting mix.

9. Inconsistent or Incorrect Timing

Starting seeds too early or too late in the season for a particular plant’s growth cycle can lead to failed germination or stunted growth.

10. Disturbance or Disruption

Some seeds require specific conditions and might be sensitive to disturbance or handling, preventing successful germination.

Read the seed packets well a few times before sowing seeds and make sure you don’t move them around after you get them under the grow lights.

If seed trays must be moved, be really really REALLY careful and I’d wait until well after germination before attempting to relocate trays.

11. Starting More Than One Variety Per Cell Tray

It is strongly recommended to do one flower variety per cell tray. This is a GREAT tip because I’ve made the mistake of condensing different plants and varieties in the same cell tray and they germinated at different times, while some didn’t germinate at all. So it is important to have enough cell trays for each packet of seeds.

By understanding these potential issues, gardeners can take proactive steps to address them and significantly increase the success rate of indoor seed starting. It’s about creating the ideal environment and conditions for each type of seed to thrive.

Good thing I saved some trays with containers from the nursery last year for this very purpose.

Quick Tips for Sowing Seeds Indoors

• Fill each of the cell or pots with pre-moistened seed starting soil. Pack it down to remove any air bubbles and gaps.
• Sow seeds according to seed packet directions. How deep you sow will depend on the seed variety. As a general rule, plant seeds twice their depth.
• Drop seed in hole then back fill with vermiculite. Depending on the type of seed, drop 1-2 seeds into each hole until the tray is completely full. It’s OK to cover with seed starting soil, but vermiculite is easier for seedlings to grow through.
• Label your seed trays and/or individual pots. Cover seed trays with plastic dome. Then place trays on heat mats under grow lights.

When to Start Seeds Indoors Chart

Now that we know what it takes to start seeds indoors, when do we begin to sow them? And the answer is, it depends upon what you are growing.

So read the seed packets and determine how long seeds need to be sown before YOUR last frost date. For me, my last frost date is typically in mid-May, so I count backwards from that date to determine when seeds should be sown indoors.

As an aside, if you are growing some cold-tolerant varieties, you can save some indoor growing space by winter sowing them outdoors.

Obstacle #7: Not Hardening Off Seedlings Properly Before Planting

After starting seeds indoors, it is extremely important that you harden them off before planting them outdoors. Hardening off plants means we help them transition from growing indoors or in a greenhouse environment to the outdoor elements of fluctuating weather. And if you don’t take the time do this, you’ll feel like something went wrong with your seedlings after starting them indoors.

The hardening-off process involves a gradual introduction to changes in temperature, wind, and sun exposure that help your seedlings transition to a firmer, harder, and sturdier plant without the shock from environmental changes.

Thus, the overall goal of hardening off plants is to slow their growth to help them adjust to outdoor living.

If you skimped on this process, seedlings may decline or worse die when you plant them in the garden because they haven’t gotten used to living in an environment with changing conditions.

How to Properly Harden Off Plants

You should plan to start this process about two weeks before your last frost date. Here’s how to do it!

• When temperatures are at least 45-50^ᵒ move plants outdoors to a protected, shady location for two to three hours. Move seedlings indoors when they’ve reached their limit and place them in a heated garage or basem*nt.
• Work them up to two or three days in a somewhat shaded location, then locate seedlings to receive morning sun. During the two-week process, gradually increase exposure to direct sunlight.
• Don’t bring plants outside on very windy days. Seedlings are not strong enough to handle high winds.
• If temperatures are expected to fall below 45^ᵒ bring plants indoors or cover them in a cold frame.

To learn more about hardening off seedlings, with tips and tricks of everything you need to know, head over to this post here.

More About Starting Seeds Indoors

What kind of garden do you want to grow from seed? Have you ever started seeds indoors before? I would love to know more in the comments below.

And don’t miss joining my Gardening DIY and Decorating Community on Facebook for more chatter. And follow along there and on Instagram as well. There are behind-the-scenes daily things that I share on Instagram that don’t make it to the blog. Would love to see you there too!

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Want To Get More Organized to Start Seeds?

CLICK HERE to get my FREE DOWNLOADABLE PRINTABLE that will help you get organized to sow seeds this year.

Print as many pages as you want and add them to your gardening journal for ease of reference during the growing season.

Shop This Post

If you are starting seeds indoors this year and need to get supplies, I got you! You can get what you need here by clicking on the products below.

If you’ve always dreamed of bringing country charm to your home while creating a beautiful, relaxing space, I got you! Learn how to grow flowers in even the smallest of spaces with my easy-care, low-maintenance approach.

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Garden Supplies I Use

I’m often asked about the garden supplies and tools that I use most. From pruners to deer repellents, here are some of my favorites in no particular order.

• I like to use a good-quality, potting soil, garden soil, compost, and perlite when planting.
• I have used this deer repellent with great success. But now, I’m all about this deer repellent that is systemic instead of topical. This means the plant takes it in as opposed to it just smelling bad.
• Hands down this is my favorite hand-weeding tool. You can use it to get underneath roots, and loosen soil, and it cuts down on the weeding time because you work much faster.
• But I also love this long, stand-up weeding tool to really get around roses from afar.
• I like to use THIS ORGANIC FERTILIZER for roses because the blooms are more prolific and it’s organic.
• You’ll need a sharp set of pruners when working with plants and flowers. I buy a few so I can stash them around.
• I use these garden snips to deadhead and cut flowers from my gardens.
• Where pest and disease problems are concerned, if I need to, I generally use this insecticidal soap or neem oil to help control infestations depending on the issue. When using, only apply when pollinators are less active.
• This is my favorite set-and-forget slow-release fertilizer for houseplants, annuals, and container gardens.
• Whenever I stake my peonies or other plants, I generally use these grow through garden supports because they work really well and keep the blooms upright.

Click here to shop my favorite garden supplies!

Shop here!

How to Start Seeds Indoors Without a Greenhouse Series

• An Overview (you are here)
• Supplies for Starting Seeds Indoors Without a Greenhouse
• 7 Simple Tips to Getting Organized Before Starting Seeds Indoors
• What You Need to Know About Sowing Seeds Indoors
• 7 Lessons I Learned Starting Seeds Indoors
• What You Need to Know About Hardening Off Plants
• How to Plant a Garden After Starting Seeds Indoors
• 7 Lessons I Learned From Growing a Cut Flower Garden
• How to Keep Fresh Flowers Longer
• Cut Flower Gardening for Beginners

Want to Learn How to Grow a Cut Flower Garden?

Would you like to learn how to grow a cut flower garden this year? I can’t tell you how rewarding it is to grow your own flowers to cut and enjoy bouquets all season long.

And while I strongly suggest starting a cut flower garden from seed, you don’t have to. But you will be more limited to what’s offered at your local nurseries.

From starting seeds to planting and cut flower arranging, this post is for you! Follow these cut flower gardening tips and be sure to check out my best advice for beginners at the end of this post.

Follow THIS cut flower gardening guide for beginners.

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About Me

Want to learn more about me?

I’m a master gardener who’s been gardening and growing things for over 25 years and author of the best-selling book, The Bricks ‘n Blooms Guide to a Beautiful and Easy-Care Flower Garden. With a deep passion for gardening, I enjoy helping others find their inner green thumb with all things plants and flowers, as well as finding ways to bring the outdoors inside their homes.

Get the inside scoop about my background as a master gardener, education, and experience, as well as why I started blogging here.

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A few years ago, I started a new cutting garden that was really fun. And, starting the flowers from seed indoors was a super cool experience that helped beat the winter blahs too.

A Beautiful Cut Flower Garden in the Pacific Northwest

My good friend Kim from Shiplap and Shells has a gorgeous cutting garden. She lives in the pacific northwest and starts many of her flowers from seed.

And Kim also has an amazing greenhouse where she starts all those seeds. Isn’t it gorgeous?