A reader asked me why their apple tree is getting yellow leaves. While I had an idea, I wanted to do more research and put together this guide to give them the best answer I could. Here’s what I found.

Apple trees get yellow leaves from over-watering, improper nutrients, transplant shock, as well as pests and diseases such as aphids and apple scab. For best results, only water when the top 2-4 inches of soil is dry, apply compost and organic fertilizer, and inspect the leaves for any signs of pests or disease.

So, while apple trees get yellow leaves for several reasons, how can we tell which issue is causing it, and from there—how can we fix it? Let’s take a closer look.

1. Seasonal

an apple tree with yellow leaves from the autumn
An apple tree with yellow and dropping leaves from the turning of seasons

Apple trees are deciduous fruit trees, so they normally lose their leaves in the fall. Usually, the leaves turn yellow and brown before they drop.

On the other hand, many evergreen trees (like citrus trees) commonly don’t experience much frost, so they keep their leaves year-round. The evergreen trees that do experience frost (like pine trees) have adapted to have other ways of surviving the winters.

By shedding their leaves, the apple trees are preserving resources so they can go dormant, waking when spring arrives (similar to a bear hibernating).

Apple trees also require about 600-800 chill hours (every hour under 45ºF) per year. This cool temperature allows them to maintain their hibernation, or dormancy. If the winter temperature gets above 45ºF, the apple trees start to come out of dormancy and can face issues if there’s another frost.

So, if your apple tree’s leaves are yellowing and dropping in the fall, know that this is normal and they’ll regrow their leaves in the springtime.

However, what happens if your apple tree is getting yellow leaves earlier in the year (spring and summer)? What could be causing it then?

2. Over-Watering

an apple tree with yellow leaves from overwatering
An apple tree with yellow leaves from overwatering

Over-watered apple trees get symptoms such as yellow and dropping leaves. The yellowing commonly comes from the stress of the roots not having enough oxygen, as well as nutrients getting flushed out of the soil.

The best way to water apple trees is to only water when the first 2-4 inches of soil is dry. You can check this by pushing a finger into the soil. If the soil is dry water it. If it’s wet, hold off on watering until it’s dry.

By only watering when the top 2-4 inches of soil is dry, you’re avoiding both under and over-watering.

However, even if you’re watering your apple tree properly, if its soil has poor drainage, you’ll need to amend it before the tree can recover.

Tip: While not as likely, yellow leaves can also be caused by under-watering. If you think this is the case for your apple tree, use the same finger test and only water when the top 2-4 inches of soil is dry.

Testing Poor Drainage

Poor drainage usually comes from soil that’s been compacted or has a high amount of clay. Because clay’s particles are smaller than sand, they compact easier and prevent water from draining through.

If you feel your apple tree’s soil and find it’s sopping wet for more than 24 hours, its soil likely needs to be amended.

You can also test your soil by doing a percolation test.

doing a soil percolation test in our backyard
Doing a percolation test in our backyard

Here’s how to do one:

  1. Dig a 1-foot by 1-foot hole
  2. Place a yardstick in the hole and fill it with water
  3. Wait 1 hour and measure how far the water has drained

If the soil is draining faster than 2 inches per hour, it has fast drainage. If it’s slower, it likely has poor drainage. However, this is a guideline and not a rule, so don’t worry if yours is off.

You can do this test a few times in different areas of your yard to get a better understanding of your soil’s drainage.

Amending Poor Drainage

If you do find your apple tree has poorly draining soil, the best way to amend it is with compost.

Interestingly, compost fixes soils with poor drainage and fast drainage. This is because compost is not only great at retaining the proper amount of moisture in the soil, but it breaks up the larger clumps of soil.

If your apple tree is fairly healthy, and only has a few yellow leaves, you can simply apply 2 inches of compost on top of the soil, under the tree’s canopy.

However, if your apple tree is losing a lot of its leaves (at least 30%), or its soil is smelling swampy (a sign of root rot), it’s best to mix in the compost and dry the soil.

For potted apple trees, I recommend repotting them with fresh potting soil.

Tip: Avoid mulching apple trees until they have well-draining soil. This is because mulch reduces evaporation, which makes poor drainage worse. Once the soil is well-draining, apply 4 inches of mulch every 3-6 months.

3. Improper Nutrients

Tyler holding Down to Earth fruit tree fertilizer
The fertilizer I use and recommend for apple trees

Excess Nutrients

Too many nutrients is usually caused by over-fertilizing apple trees. This is most common with fast-release fertilizers.

If you believe you’ve over-fertilized your apple tree, the best thing to do is to leach it through your soil. To do this, provide your apple tree with plenty of water on a slower drip. The water will carry the excess nutrients from the fertilizer lower into the soil, out of reach of the apple tree’s roots.

But what if you haven’t fed your apple tree recently—what could be the issue then?

Lack of Nutrients

Nutrient DeficiencyLeaf Symptom
NitrogenEntire leaf is pale or yellow
IronDark green veins, rest of the leaf is yellowing
ZincYellow blotches
ManganeseBroadly pale leaves, foliage color looks mottled or smeared
Source: The University of California Agriculture and Natural Resources

Like most plants, apple trees require three main nutrients: nitrogen, phosphorus, and potassium (abbreviated as NPK). However, the two most common deficiencies that cause yellow leaves are nitrogen and iron.

Iron is required for the production of chlorophyll and so a deficiency results in the absence of green pigment in leaves.

Washington State University

To help treat yellow leaves, use an organic fertilizer, which has plenty of iron. To be safe, we also supplement with kelp fertilizers (high in iron and potassium).

You can see the fertilizers I use and recommend on my recommended fertilizer page.

Keep in mind, even if apple trees have sufficient nutrients in the soil, they’re unable to absorb the nutrients properly if the pH is not balanced.

Imbalanced pH

ph scale couch to homestead

Apple trees prefer a soil pH of 5.8-7.0.

Most plants prefer a slightly acidic soil pH as it dissolves the nutrients in the soil and makes them accessible to the plant’s finer roots.

“Approximately 70-80% of nitrogen (N), 60-85% of phosphorus (P), and 80-90% of potassium (K) found in feeds is excreted in the manure. These nutrients can replace fertilizer needed for pasture or crop growth, eliminating the need to purchase fertilizers.”

University of Massachusetts Amherst

Two good ways to check your soil’s pH are either by using a pH strip or a pH meter. I prefer using a pH meter since they’re affordable and easy to use. To see which pH meter I use and recommend, check out my recommended tools page.

If you find your apple tree’s soil is too acidic (under 5.8), add alkaline amendments such as wood ash, charcoal, or lime (ground limestone).

On the other hand, if you find that your apple tree’s soil is too alkaline (above 7.0), add acidic amendments such as coffee grounds, sand, and peat moss.

Additionally, cold and/or wet soils are not good at promoting nutrient uptake as the apple tree will either be slightly dormant during the cold or too stressed in wet soils.

4. Transplant Shock

placing the fruit tree in the hole in our backyard

If your apple tree was recently planted or repotted, and it’s starting to die, it’s likely due to transplant shock. Transplant shock occurs when a plant is exposed to a new environment and has to establish a new root system.

Avoid transplanting apple trees unless necessary as it can take up to 1 year for recovery.

To help avoid transplant shock, I like to plant with the following steps in mind:

  1. Have the new ground (or pot) prepared
  2. Remove as much of the plant’s current topsoil as possible, without damaging the shallow roots
  3. Grab the base of the plant’s stem and wiggle lightly
  4. Using your other hand, scoop up and support the rootball
  5. Lightly place the plant in the new ground (or pot) and fill it in
  6. Make sure the soil is at the same level on the plant as before
  7. Apply 2 inches of compost and 4-12 inches of mulch to the top of the soil
  8. Water generously and add more soil as needed

5. Pests


aphids on an apple tree leaf
Aphids found under an apple leaf

Aphids are small bugs that suck the sap from underneath the lemon tree’s leaves. This loss of sugar and moisture causes the leaves to curl, discolor, and drop. Aphids also deposit honeydew, which attracts ants.

If left unchecked, aphids can damage the lemon tree’s health and potentially stunt or kill it.

These bugs come in multiple colors including white, yellow, or black, and usually are found hiding underneath the leaves. Typically, aphids won’t cause damage to the fruit, but because they suck sap from the plant, they can compromise its health and therefore reduce fruit size and yield.

The best ways to get rid of aphids (and spider mites) on lemon trees is by spraying the infected leaves with water or neem oil, or releasing ladybugs (a natural predator of aphids and mites). Most often, a jet of water is enough to knock them off and kill them, but neem oil is a good second option.

For example, when my potted Kaffir lime tree had aphids, I found that a jet of water was sufficient to blast them off and prevent them from coming back. All I did was remove the hose nozzle and used my thumb to increase the pressure. Just keep in mind that too strong of a blast can damage the leaves.

To attract ladybugs to your garden, you can plant apple tree companion plants such as dill, fennel, and yarrow.

6. Diseases

Out of these three apple tree diseases, root rot and powdery mildew are most common to show as solid yellow leaves, while apple cedar rust commonly shows as yellow spots. Let’s take a closer look at the symptoms and treatments for these apple tree diseases.

Root Rot

tomato plant with Phytophthora root and crown rot
A tomato plant with root rot

Root rot, also known as Phytophthora root and crown rot, is a fungus that starts in the soil before spreading to the apple tree’s roots. Over time, leaves, fruit, and branches become affected.

Symptoms of root rot on fruit trees include:

  • Brown and rotting branches, leaves, and fruit
  • Yellow leaves
  • Leaves and fruit dropping
  • Sopping wet and swampy-smelling soil

The most common cause of root rot is overwatering or soil with poor drainage. Because of this,

If root rot is left for too long, the roots will decay, killing the rest of the tree. Fortunately, root rot can be prevented and treated by allowing for proper drainage and drying out the soil.

For example, my potted Kaffir lime tree suffered from root rot. After discovering that the soil smelled like a swamp and wasn’t draining, I repotted the tree with fresh potting soil. From there, it was a quick recovery!

So, if your planted apple tree is affected by root rot, hold off on watering and amend the soil to increase drainage.

You can amend your apple tree’s soil by adding 2 inches of each sand and compost, or by transplanting the tree to a mound or raised bed.

Powdery Mildew

powdery mildew spores on a leaf

Powdery mildew is a fungal disease that appears as small white spots (spores) on the apple tree’s leaves. It causes apple tree leaves and twigs to curl, yellow, and die, as well as leaves and fruit to drop.

This issue is made worse in areas with high humidity and poor ventilation.

For example, if your apple tree’s canopy is thick, it’ll have reduced airflow and sunlight—promoting fungal diseases such as powdery mildew.

You can control or prevent powdery mildew by pruning to improve ventilation and sunlight and using a spray (I recommend saving this as a last resort).

To start, prune overlapping or clustered branches. Pruning an apple tree’s canopy also trains it to spend less energy on foliage and more on fruiting (great for mature apple trees). It also allows it to grow more fruit on fewer branches.

Avoid over-pruning as it weakens the tree and can make its recovery harder.

Cedar Apple Rust (Yellow Spots)

yellowing apple leaf with cedar apple rust disease
If your apple tree’s leaves have yellow spots, then it’s likely a type of disease. The most common is Cedar Apple Rust (pictured above).

Apple cedar rust is a fungus that spreads from juniper trees (also called cedars) to apple trees. The spores are carried from one tree to another in the spring when it’s warmer and rainy. This disease is most common in the Northeast US and especially affects more rural areas that have both farmland and forests.

While cedar apple rust is a common recurring issue, it can be treated by reducing nearby juniper trees, growing resistant apple varieties, and using sprays.

Symptoms of apple cedar rust include:

  • Yellow Leaves
  • Yellow Spots on Leaves

You can help reduce the fungus from spreading if you clear the weeds in at least a 6-foot radius around your apple tree.

Also, consider growing apple tree varieties that are resistant to this disease, such as ‘Red Delicious’, ‘McIntosh’, ‘Arkansas Black’, ‘Winesap’, ‘Mollies Delicious’, ‘Spartan’, ‘Priscilla’, ‘Liberty’, and ‘Empire’.

If those fail, consider using a fungicide spray.

“Follow a recommended fungicide spray schedule, beginning at the pink-bud stage of growth and continuing every 10 to 14 days through the first or second cover spray.”

Apple National Cooperative Extension Resource

When considering chemical sprays, contact your local cooperative extension for recommendations on application and timing.

For a safe spray to use, while there are not a lot of truly organic sprays out there, many growers are finding success in treating cedar apple rust and other apple tree diseases with homemade sprays containing whey.

If you’d like to learn more about a safe and effective spray for cedar apple rust and other orchard diseases, check out this video by Stefan Sobkowiak – The Permaculture Orchard.

Final Thoughts

After trying some of the suggestions, my reader found that her apple tree was getting over-watered. Once she allowed the soil to dry out before watering, her apple tree made a recovery!

After working through the above solutions, your apple tree’s yellow leaves should fall off and grow new, shiny green leaves.

If you’ve tried all of the above, and you still don’t have a solution, I wrote a post on how to save an apple tree in 3 steps, so make sure to check it out.



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