Of all the challenges that can occur when growing fruit trees, diseases in fruit trees are one of the most common concerns for home growers.

Spots on leaves, wilted branches, or rotting fruit are never a good sign! They’re often the first way your tree signals that all is not well.

Diseases in fruit trees are one of the most frequent issues home orchardists face, and we know it can feel overwhelming when your trees just won’t stay healthy. 

While diseases can be caused by different things, such as fungal infections, bacterial problems, viral issues, or environmental stress, understanding what you’re dealing with is the first step to healthier trees and abundant harvests.

The most common diseases in fruit trees

After growing a wide range of fruit organically since 2008 (and working with thousands of backyard fruit growers), we’ve learned that most fruit tree diseases fall into just three categories.

Understanding the “big three” disease types will help you become a better fruit tree detective. Here’s what causes most of the disease problems you’ll encounter:

Fungal diseases

Fungal diseases are by far the most common issues in home orchards. These include problems like brown rot, powdery mildew, and apple scab.

Fungi love warm, humid conditions and can quickly spread through your orchard if left unchecked. The good news? Most fungal diseases are very preventable with the right approach.

Bacterial diseases

Bacterial diseases like bacterial canker can be more serious, especially for stone fruit trees. If you live outside Australia, fire blight is an insidious risk, especially for apple and pear trees. These diseases often enter through wounds or natural openings and can kill entire branches if not caught early.

Viral diseases

Viral diseases are less common but can affect tree vigour and fruit quality over time. Unfortunately, there’s no cure for viral diseases, so prevention through healthy growing practices is key.

Preventing diseases in fruit trees

Here’s the truth. Preventing diseases is always easier than treating them! Whether or not you get disease problems isn’t random—it depends on your growing practices and how well you understand your trees’ needs.

The foundation of disease prevention starts with these key principles:

• Choose the right varieties: Some fruit tree varieties are naturally more disease-resistant than others. When we plant new trees, we look for varieties bred for disease resistance in our climate, so make sure you are looking at your local conditions.
• Proper spacing and pruning: Good air circulation is your best friend when it comes to preventing fungal diseases. Proper pruning helps sunlight and air reach all parts of your tree.
• Soil health: Healthy soil creates strong, resilient trees that can naturally fight off disease problems.
• Timing matters: Many diseases can be prevented with well-timed organic sprays applied at the right moments in your tree’s growth cycle.

Apple tree diseases

Apple trees are prone to several common diseases, with black spot (also called apple scab) and powdery mildew being the most frequent problems. Fire blight can also be serious in some regions, but luckily not in Australia (yet)!

The key with apples is choosing scab-resistant varieties if you live in a humid climate. This one decision can save you years of frustration!

Stone fruit diseases

Peaches, nectarines, plums, and cherries (link: new page) share many of the same disease problems. Brown rot is the biggest concern, especially as the fruit ripens. Peach leaf curl is another common fungal disease.

Stone fruits benefit enormously from preventive organic spray programs, especially in humid climates.

Access more on solutions for stone fruit tree diseases.

Citrus fruit tree diseases

Citrus trees have their own set of disease challenges, including citrus canker, root rots, and various fungal problems. Many citrus diseases are related to watering issues—either too much or too little.

The good news is that well-cared-for citrus trees in the right climate are generally quite disease-resistant.

Organic treatment options

When prevention isn’t enough, there are effective organic treatments that align with sustainable growing practices:

• Copper sprays: Excellent for fungal diseases, especially when applied preventively. Can also be used for bacterial diseases, though are less effective.
• Sulphur-based treatments: Great for brown rot, powdery mildew, and other fungal issues. A relatively “soft” option with less risk of harming the soil. 
• Biological controls: Beneficial microorganisms that can help suppress disease problems naturally.
• Cultural practices: Sometimes the best “treatment” is improving growing conditions—better drainage, improved air circulation, or adjusted watering.

When to take action

Not every spot or blemish on your tree means disaster. Learning when to worry and when to stay calm is part of becoming a confident fruit grower.

Act quickly if you see:

• Rapid wilting of branches (possible bacterial blight, or could be fire blight if you’re outside Australia)
• Widespread leaf spots that are spreading quickly
• Fruit rot that’s affecting multiple fruits
• Any symptoms that are getting worse rapidly.

Monitor but don’t panic if you see:

• A few spotted leaves here and there
• Minor cosmetic issues on the fruit
• Symptoms that appear after stress (like drought or extreme heat).

The key is regular observation. Visit your fruit trees to say g’day at least weekly during the growing season, and you’ll catch problems early when they’re easiest to manage.

Why disease management matters

Focusing on having healthy trees isn’t just about avoiding problems—it’s about creating the abundant harvest you’re dreaming of.

When diseases are under control, your trees can put all their energy into producing delicious, nutritious fruit. Disease-free trees are also more resilient to other stresses like drought, pests, and extreme weather.

Most importantly, once you understand how to prevent and manage diseases, fruit growing becomes so much more enjoyable. Instead of worrying about what might go wrong, you can focus on the joy of growing your own food.

The role of seasonal care

Managing diseases in fruit trees isn’t a one-time job—it’s woven throughout your seasonal care routine.

Winter: This is prime time for dormant season spraying and removing any diseased wood through pruning. It’s also the perfect time to feed the soil with rich compost (ideally home-made).

Spring: Spring spray programs can prevent many fungal diseases before they get started.

Summer: Regular monitoring and good watering practices keep trees strong and resistant to disease.

Autumn: Post-season cleanup removes disease sources before they can overwinter and cause problems next year.

Need more help? Check out more resources about fruit tree health.

Grow Great Fruit Program

Are you worrying about the leaves on your fruit trees? Let’s get to the bottom of that—and set you up for your best fruit-growing year yet.

In the Grow Great Fruit program, we help you tackle leaf problems and we give you skills to grow healthier trees and bigger harvests across your whole orchard.

Each week you get a checklist of seasonal jobs to prevent issues before they start. There are step-by-step videos and guides on pruning, pest and disease prevention, and every other fruit growing topic.

Need answers? The Members Forum is full of answered questions from other growers who’ve been in your shoes. And Premium members get personal answers to questions from us for quick, expert support.

Let’s get your fruit trees thriving—this season and beyond.