Why Are My Seedling Leaves Yellow?

It's magic. Tiny little seeds go into their new homes in your seed-starting tray, and a few days later, green shoots pop up. At first, they seem to grow quickly, but then they stop, and now the tomato seedlings you were proud of are causing you anxiety as they start to turn yellow. What gives? 

First, don't lose hope. I've planted many less-than-perfect-looking seedlings into my veggie and flower gardens and had them perk up in a week or ten days to become healthy plants. That may be because my garden soil is healthy, well-drained, and teeming with beneficial microbial life, which does the job for me. In the seed starting room, it's all up to me (you). 

Yellowing seedling leaves are a blinking warning sign telling you something isn't quite right. Healthy seedlings are green, stout, and lush-looking. The sooner you catch the problem, the better for the plant and, ultimately, your harvest. Low vigor plants mean lower yields. Check on these issues if your seedlings are looking a bit under the weather and yellowing.

Five Common Reasons Seedling Leaves Turn Yellow

Yellow seedling leaves can be frustrating, and the problem may turn out to be two or more issues at the same time. Check out these ideas below and work to fix them, and your seedlings will likely be on the mend in a few days. 

Watering Issues (Overwatering & Under-watering)

Probably the most common human-caused error in growing seedlings is improper watering and moisture levels. We're afraid of under-watering, so we keep them too wet! 

Overwatered seedlings often start to turn yellow, usually from the lower leaves first. The stems may look soft, and the entire plant can get droopy. This can be solved in most cases by simply scaling back on the watering frequency. Let the soil dry slightly between waterings and water from the bottom.

We always fear under-watering our seedlings, especially in small cells or soil blocks. As seedlings get larger, dry conditions can happen rapidly. Wilting and sometimes yellowing leaves from too little moisture start at the top of the plant. Feel the soil mix with your fingers—if it's dry and lightweight, you probably need to water it. As seedlings get larger, they'll use more water per day, and being stuck in a small, fixed soil volume means they'll dry out quicker. Six-inch tall tomato seedlings ready to transplant need watering much more often than when they were just an inch tall with four tiny leaves.

Inadequate Light

Every other article about indoor plant problems seems to blame them on a lack of light, and that's for good reason. Although we often refer to fertilizer as "plant food," it really isn't. Fertilizers provide components in the tools used to make food. It'd be akin to calling your stove and frying pan people food and forgetting about the chicken or peas. 

Plants make their own food from water, carbon dioxide, and light. Without sufficient light, they can't make their primary food. Without food they can't continue the other processes that use energy to rearrange minerals and nutrients into vital structures like chloroplasts, cell walls, and pigments (chlorophyll).

Seedlings need lots of light; a bright, sunny window may not cut it. Provide 12–16 hours of bright supplemental lighting and see if they perk up. Remember you'll need to water them frequently under artificial lighting, as they'll be more active and take up additional water.

Transplanting Shock

Cranky seedlings that look like you're slowly killing them right after transplanting can be caused by root damage or environmental stress. They may wilt and yellow a bit for those first few days, making you think you've doomed them. Fortunately, they usually recover. To minimize transplant shock, be sure to harden them off appropriately before transplanting. They’ll be accustomed to their new environment and establish faster.

Rootbound seedlings in their pots are another common problem for larger seedlings. Damaged roots from transplanting need a little time to regrow, which can cause sad-looking seedlings. Potting up seedlings into larger containers or cells before they become rootbound can help.  

Root Problems

While it's easy to assume that yellow leaves mean a nutrient deficiency and reach for fertilizer, soil drainage and root issues are common causes of yellowing leaves and poor seedling performance. Growing medium problems cause root problems. Without healthy roots, you won't have a healthy plant. 

Poor drainage is a leading cause of seedling issues for home gardeners. It invites fungal issues and creates soggy conditions that keep roots from absorbing oxygen. You read that right. While we remember from grade school that plants take in carbon dioxide and release oxygen from their leaves, the roots also take in oxygen to perform cellular respiration. Without it, they can't feed themselves and run low on energy. Like us, roots with low energy levels don't perform their functions well. Soggy, poorly drained soil causes a low oxygen condition at the roots. 

Damaged or compacted roots are another culprit. Given that unhealthy roots lead to unhealthy plants, it stands to reason that damaged or compacted roots aren't able to do their jobs well. Roots that can't take up nutrients efficiently won't be able to keep up with the plant's above-ground needs, and the resulting stress often shows as stunted growth and yellowing leaves. 

Nutrient Deficiencies

Nutrient deficiencies are a common cause of yellowing leaves, and the pattern in which they turn yellow can explain what might be missing. Low levels of nitrogen, phosphorus, potassium, iron, and magnesium can all cause leaves to turn yellow, especially tomato leaves. 

Low nitrogen levels often present as older leaves (typically those on the bottom of the plant) yellowing and eventually dropping off. Symptoms of a nitrogen deficiency include yellow-green or yellowing color and slow growth. Phosphorus deficiency in seedlings is shown in stunted growth and yellowing leaves with a purple tinge on the underside of the leaves. Potassium deficiency also shows as yellow leaves. 

Because many (most) purchased seed starting mixes are soil-less, they do not contain actual soil and can be low on nutrients. Often, they are a mix of finely ground peat, coir, bark, and wood, as well as perlite, to keep them fluffy and aid in drainage. Seed starting mixes are often manufactured to be sterile and low in fertility.

In the early days, the nutrients required to get your seedlings up and running are contained in the seeds. However, eventually those stores of energy will be exhausted and need to be provided by the soil. Plants require nutrients to assemble the complex molecules that build their structure. For example, the chemical formula for chlorophyll-a is C₅₅H₇₂O₅N₄Mg. Without nitrogen and magnesium, the plant can't make a chlorophyll molecule.  

Some seed-starting mixes have very low fertility, while others come out of the bag with enough nutrients to last seedlings a month. However, if you are seeing the above symptoms of low fertility, you can use a diluted general-purpose fertilizer when watering to address the issue. Follow the directions on the package and apply weekly. 

Many gardeners mix compost with their seed starting mix to alleviate any nutrient issues. While this has the potential to introduce pathogens, the risk is low if using commercially prepared compost. These bagged products are heated to a temperature high enough to kill most problem microbes. Homemade compost may or may not have reached that temperature, so be cautious.

FAQs About Yellow Seedling Leaves

What if the first two leaves are yellow, but the rest look fine?

If the cotyledons, often called seed leaves, are yellowing, but the true leaves look good, you're okay. Seed leaves aren't meant to stay with the plant forever. They commonly yellow and fall off after the plant has grown regular leaves and doesn't need them anymore. You can pinch them off or wait for them to drop on their own. 

Can yellowing leaves turn green again?

Most of the time, a yellow leaf will not return to green, healthy conditions. However, if it was caused by nutrient deficiencies and treated early, they may. Correcting the problem will likely result in new, green growth instead.

My tomato seedlings have purple veins. What's the problem?

Purple-tinged leaves, either veins or on the underside of the leaf, are common with tomato seedlings grown at home and indicate a lack of phosphorus. This factsheet from the University of New Hampshire has an excellent image of what that looks like. Apply a diluted fertilizer solution and they’ll cheer up.