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11 Causes of Yellow Spots on Lemon Tree Leaves (And Treatment)

Nothing is more appealing than growing your lemon tree, with the promise of lemons and the smell of its flowers.

Leaves on lemon trees tend to be glossy green, but they lose their lush appearance and health if they develop unsightly yellow spots.

Leaf blight, rust, citrus canker, powdery mildew, and greasy spot disease are the most common causes of yellow spots on lemon tree leaves. The treatment is to cut off the affected leaves and spray them with a fungicide. Yellow leaf spots can also be caused by pests, nutrient deficiencies, and inadequate watering.

Sometimes the culprit is easy to fix, but not always. The size, shape, and pattern of the yellow spots, as well as a review of how you care for your lemon tree, can help you figure out what’s wrong and fix it.

[1] Citrus Canker

Lemon trees aren’t too susceptible to diseases, but citrus canker is a common problem that can cause yellow spots. A bacterial pathogen usually causes the disease.

However, bacterial citrus cankers are more common, more serious, and can be fatal to most varieties of lemon trees, including Meyer lemons.

The bacterial infection causes lesions on almost every part of the tree, including fruits, stems, and leaves.

Fruits drop prematurely, twigs die back quickly and leaves rapidly shed in severe cases.

As a result, the fruits are usually severely damaged, and the overall health of your lemon tree suffers.

Early symptoms of bacterial citrus canker include yellow spots on the leaves.

Small, slightly bumpy blisters on the undersides of leaves are usually the first signs of infection.

Lemon trees that grow outside will likely get citrus canker within the first three months after their flowers fall off.

With time, these lesions turn tan to brown with watery yellow margins. Additionally, you might notice brown lesions with yellow edges on twigs and fruits that are water- or oil-soaked.

These lesions become corky or appear like fruit scabs as they age.

Leaf lesions are visible on the foliage’s upper and lower surfaces.

Their centers are usually corky and raised. Most of the time, when these lesions fall out, they leave round, dead holes.

As the infection spreads and becomes more severe, your lemon tree may suffer rapid and widespread leaf loss.

In addition, the disease is contagious and often spreads quickly through windy rain and unintentional contact with people as they move.

Treatment and Prevention of Citrus Canker

Cankers on citrus trees can be hard to eliminate, mainly if bacteria cause them. However, you can try using a suitable fungicidal spray to treat the problem.

I’ve found that sprays based on copper (Amazon link) are effective in mild to modest disease cases.

Give it suitable spraying if you notice any cankers on your tree. Ensure that the fungicide is completely covered on any exposed fruits.

If you’re spraying lemon trees outside where it rains, you may have to repeat the process twice.

[2] Lemon Tree Greasy Spot Disease

Greasy Spot Disease Symptoms

Greasy spot disease is one of the most common causes of yellow spots on lemon tree leaves.

It’s a fungal disease that makes your lemon tree more susceptible to other infections, pests, and cold damage.

Most of the time, the spores of greasy spot fungus grow on the undersides of leaves, causing swollen blisters.

The leaves upper surfaces will first show yellow spots, followed by brown lesions with odd shapes.

It is common for the greasy and bumpy dark brown blisters to first appear on the undersides of leaves before moving up to the upper surfaces.

Once a leaf is fully open, it is more susceptible to the fungus and remains so throughout its life.

Affected leaves may fall off before any of the above symptoms appear.

Treatment and Control of Greasy Spot Disease 

Copper-based fungicides are the best way to treat and keep greasy spot fungus from spreading on lemon trees.

I make mine by mixing two to four teaspoons of copper powder into a gallon of water.

When mixing your own, be sure to adhere to the mixing instructions found on the product label.

As soon as you notice the first signs of disease on your tree, spray it liberally with copper spray. Don’t forget to cover the undersides as well.

Spray your lemon tree with fungicide every 1-2 weeks until the fungus is gone.

[3] Lemon Tree Leaf Blight

Leaf blight is a fungal disease that affects lemon trees in warm, moist conditions.

Fallen leaves and other dead plant matter are common locations for fungal spores to survive the winter.

It usually gets into your indoor lemon tree through the water you use to water it.

Lemon tree leaf blight symptoms are most severe on leaves near the ground.

However, it’s even more common if you’ve given your lemon tree in a pot too much water.

Initially, brown water-soaked lesions surrounded by a yellow halo appear on lower and older leaves.

Because of this, the leaves look decorated with yellow rings in the shape of a target with brown centers.

As the disease worsens, the leaves will turn black, curl up, and die before falling off. The youngest and oldest lemon trees are the most susceptible to leaf blight.

Treatment and Control of Lemon Tree Leaf Blight

Lemon tree leaf blight can be controlled by treating the affected trees as soon as symptoms appear.

Then, use a sterile pair of pruning shears to remove any affected leaves.

After that, I advise using a copper-based fungicide to spray your lemon tree thoroughly.

Use a generous amount of fungicidal spray on the undersides and tops of all leaves.

Use ready-to-use Anilazine or mancozeb-based products (Amazon link) to spray. Spray once every week or two weeks.

[4] Citrus Scab Disease

Citrus Scab Disease

Citrus scab, a common fungal disease that affects lemon trees, begins as yellow spots that quickly turn into scab-like lesions.

There are a variety of scabby lesions that appear on fruit, leaves, and even shorts infected by the fungus.

These lesions are typically pink, which is the color of pustules. However, the pink lesions will eventually turn yellow-brown and black as the disease progresses.

Citrus scab disease often has the most significant impact on fruits. This is because many scabs can be on a single fruit, causing it to become wrinkled, bumpy, or distorted.

Control and Management of Citrus Scab in Lemon Trees

Apply three applications of copper-based fungicidal spray to your infected lemon as follows:

  1. Apply for the first time when a quarter of the flush spring leaves appear.
  2. The second application should take place during the petal fall.
  3. Three weeks after the second spray, apply the final one.

Mix two to four teaspoons of copper fungicide into a gallon of water to make a copper spray.

Follow the manufacturer’s instructions, as they may differ from product to product.

[5] Powdery Mildew

Powdery mildew is a fungal disease that causes the white powder to cover the leaves of your lemon tree.

This problem thrives when your lemon tree is exposed to excessively humid conditions. It likes it when there isn’t enough airflow, and the plants are too close together.

The powdery substance is most visible on the upper surfaces of leaves, but it can also be found on the bottom and top sides of foliage.

Pale yellow spots on lemon tree foliage are among the first signs of a fungal infection.

They’ll eventually turn into tiny powdery circles. The fuzzy white substance may cover the entire leaf as the situation worsens.

Aside from the powdery white spots, powdery mildew can be identified by discolored, curled, or shriveled foliage.

In addition, due to fungal takeover, severely affected leaves may begin to turn yellow or brown.

Powdery mildew thrives from 60 to 80°F (15 to 27°C). Unfortunately, it’s also very contagious and spreads quickly to trees and plants nearby.

Treatment and Control of Powdery Mildew

You can get rid of and treat powdery mildew using any of the following methods:

Baking soda solution 

Combine three tablespoons of neem oil and 1.5 tablespoons of baking soda in a gallon of water.

This home remedy alters the pH of the leaf surface, making the fungus that causes powdery mildew unwelcome. A weekly application should suffice.

Compost tea solution

The compost tea solution is another effective yet simple home remedy I use to treat powdery mildew. In addition, it has potent antifungal properties.

You can buy a compost tea kit (Amazon link) or make it yourself:

  1. Mix 1 part aged compost plus five parts of water.
  2. Let the mixture sit for one to two weeks.
  3. Strain out the compost and dilute the liquid until it takes the color of tea brew.
  4. Use the compost team solution to spray your lemon tree biweekly.

Neem oil 

Neem oil and other horticultural oils are godsends for gardeners. Apply neem oil to the leaves until they are glistening. It is best to repeat the process every 7-14 days.

Powdery mildew can make your eyes and skin itch if you touch it directly.

Make sure to wear long pants, long sleeves, a respirator mask, waterproof gloves, and eye protection to keep yourself safe.

[6] Root Rot

Your lemon tree’s roots are susceptible to rot, even though it’s a hardy species.

When the roots of your tree are weak or malnourished, fungus and bacteria can quickly take over and destroy your tree.

Root rot can also cause yellow spots on leaves because of nutrient deficiency.

Lemon trees are commonly affected by two types of root rot.

Armillaria root rot 

This fungal disease is caused by the fungus Armillaria mellea. Common symptoms may include:

  • Your lemon tree has suddenly wilted.
  • The health of your tree is deteriorating or collapsing.
  • Yellowish-brown spots appear on the leaves, which then fall off.
  • The tree’s bark is rotting at the base.
  • Mushy roots emit a foul odor beneath the soil.

Black root rot 

Caused by the fungus Thielaviopsis basicola, black root rot manifest in the following symptoms:

  • Leaves turn yellow and wilt.
  • Leaf drop because of severe rot.
  • Stunted growth. (Here is how to fix slow growth issues)
  • Small, black, or dark brown lesions appear on roots. Soon, they’ll merge, turning the whole root black.
  • Roots become mushy, and the out layer peels off easily.

Control and Treatment of Root Rot in Lemon Trees

Sprays that kill fungi don’t work well on either black root rot or Armillaria root rot.

Instead, cut off the affected roots, drench the remaining ones in a fungicidal drench, and replant in well-draining soil. Overwatering should be avoided.

[7] Improper Watering

Lemon trees are moisture-loving plants, and a lack of water significantly impacts their health and growth.

However, both underwatering and overwatering can cause yellow spots and yellow leaves.

Watering issues and nutrient deficiencies frequently coexist.

And this usually leads to yellow spots, especially if your lemon tree doesn’t get enough nitrogen, magnesium, or iron.

Overwatering causes irreversible damage to the root system. This reduces the ability of your lemon tree to absorb and transport essential nutrients.

Signs of a dehydrated lemon tree include:

  • Leaf tip browning.
  • Death or withering of new growth.
  • Leaves feel inflexible, dry, and crunchy.
  • Leaves falling off.
  • Excessive curling of leaves.

On the other hand, a lemon tree that gets too much water suddenly droops, its leaves turn yellow, and it gets brown spots that may have yellow rings around them.

The presence of root rot is indicated by smelly, soggy soil that does not dry out.

How to Fix

It is critical to grow your tree in well-draining soil and to ensure that the container has enough drainage holes.

Furthermore, remember to empty the cachepot or drip tray after watering so that the rootball does not sit in wet soil for an extended period.

Water your lemon tree thoroughly until fluid emerges from the drainage holes.

Check the soil moisture every 1-2 days and water when the top 1-2 inches of soil become dry.

[8] Pest Infestations

Although pest-resistant, lemon trees can still be infested with insects, causing your plant to show damage signs such as yellow spots.

This is particularly true of sap-sucking insects such as mealybugs, aphids, and leaf miners.

Leaf Miner Damage

Yellow spots on lemon tree leaves may indicate pests sucking vital juices from the foliage.

In addition, spider mites frequently leave yellow stippling on vegetation, which is not always visible.

Scale insects resemble miniature helmets on foliage and bark. They are known for sucking sap from fruits and vegetation, leaving yellow spots on the leaves.

In addition, they excrete honeydew, which attracts ants and causes black spots.

Aphids, mealybugs, and leafhoppers are all the same.

Stink bugs, like spider mites, leave yellow stippling on leaves, emit a foul odor, and cause brown spots. Thrips as adults can appear as yellow-orange dots or spots.

How to Get Rid of Lemon Tree Bugs

The correct method to use will depend on the specific bug. Generally, you can use:

  • Natural predators like green lacewings.
  • Horticultural oils like neem oil.
  • Non-toxic pesticides like pyrethrins.
  • Rubbing alcohol (use cotton swabs to dub mealybugs and other wax-coated bugs)
  • Yellow traps.
  • Insecticide application.

[9] Cold and Frost Damage

Only lemon trees grown in USDA zone 9 are hardy. However, in colder climates, they will suffer frost and cold damage.

The yellow spots on the leaves were caused by magnesium deficiency, which was triggered by cold roots.
Typical for trees, experiencing hot days and cool nights with a wide range of maximum temperatures.


  • To detect cold damage in your lemon tree, use a black light.
  • Remove any weeds and mulch around your tree.
  • Consider wrapping a warm blanket around the top of your plant.
  • Place a small heater near your lemon tree to keep it warm.

[10] Nutrient Deficiency

A lack of magnesium or zinc can cause irregular yellow spots on the leaves of your lemon tree.

If you notice yellow blemishes on the leaf margins, your tree may be deficient in magnesium, which occurs when the soil pH falls below 5.0.

Zinc deficiency is most likely the cause of yellow spots on the veins of the leaves.


  • If the leaf has yellow spots, but the vein is green, use Epsom salt. Here is how to do it.
  • Spraying zinc sulfate solution on the leaves will compensate for the lack of zinc.
  • Adjust soil pH with lime to the 6.0-8.0 range to correct magnesium deficiency.

[11] Edema in Lemon Tree

Yellow spots are sometimes caused by edema. Yellow halos surround watery brown blotches.

As the edema problem worsens, you may notice slightly raised, water-soaked lesions on the backs of leaves.

This is because they serve as a breeding ground for bacterial and fungal leaf spots, resulting in yellow spots.


Edema is commonly caused by overwatering. Because its effects are irreversible, consider trimming off any affected foliage.

Reduce watering until one to two inches of soil is dry, then increase air circulation.

How to Prevent Yellow Spots on Lemon Tree 

  • Maintain a good watering routine by allowing 1-2 inches of topsoil to dry before watering again.
  • Maintain a healthy and well-fed lemon tree.
  • Remove pests as soon as they appear.
  • Allow plenty of light in through a south-facing window.
  • Make sure the soil drains well.
  • Maintain temperatures of 75-85°F (24-29°C) and humidity levels as close to 50% as possible.
  • To ensure adequate ventilation, prune your lemon tree.

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