The Top 5 Onion Diseases (and How to Prevent Them Naturally)

A Lesson From the Onion Patch

One wet spring, I thought I had the best onion crop of my life. The tops were green, thick, and stood like soldiers in rows. But by mid-summer, half the leaves had collapsed, yellowed, and were covered in a strange fuzz. By the time I pulled them, many bulbs were soft and useless. That was the year I learned onions aren’t as tough as they look—they’re one of the most disease-prone crops in the garden.

The good news? Most onion diseases can be stopped before they ruin your harvest. If you know what to watch for and act early, onions can be one of the most reliable crops on your homestead. Let’s break down the five worst diseases and how to beat them naturally.

Understanding Onion Diseases

Onions are shallow-rooted and highly sensitive to excess moisture and poor airflow. Fungal and bacterial pathogens thrive in damp leaves or heavy soils, which makes prevention more important than cure.

• Cool, damp Zones (4–7): downy mildew and storage rots are the biggest risks.

• Warm Zones (8–10): soilborne diseases like basal rot and white rot show up more often.

Wherever you are, the principles are the same—rotation, airflow, and vigilance.

1. Downy Mildew

Symptoms: pale patches on leaves, later covered with gray-purple mold. The leaves twist, collapse, and bulbs stop growing.

Step-by-step prevention:

1. Space plants 6–8" apart for good airflow.

2. Water at the soil level in the morning, never overhead.

3. Apply organic sprays like copper or neem at the first sign of infection.

Pro Tip: Don’t plant onions after garlic or leeks—these cousins share the same pathogens and will spread it faster than you think.

2. Purple Blotch

Symptoms: small, water-soaked spots that quickly turn purple with yellow halos. They spread rapidly in humid conditions.

Prevention steps:

• Rotate onions out of the same bed for 3–4 years.

• Choose resistant varieties if available.

• Use drip irrigation so the foliage stays dry.

Grandma’s Tip: “Don’t crowd your onions—plants need elbow room just like people.”

3. Neck Rot

This one doesn’t usually show in the field—it sneaks up later in storage when you think your onions are safe.

Prevention steps:

• Cure onions completely: dry for 2–3 weeks in a warm, airy place until the necks are tight and papery.

• Never store onions with thick, green necks—they’re not ready.

• Store at 32–40°F with steady airflow.

Avoid This Mistake: Storing onions in sealed plastic bags. They need to breathe. Mesh bags or wooden crates are your friend.

4. Fusarium Basal Rot

Symptoms: yellowing outer leaves, bulbs rotting from the base upward. Slice open a bulb and you’ll see a brown, mushy core.

Prevention steps:

• Improve drainage—raised beds help if your soil stays wet.

• Sanitize tools and don’t reuse soil where rot has occurred.

• Rotate out of onions and garlic for 4–5 years.

This one is tough to stop once it starts. Healthy soil and sanitation are your best defenses.

5. White Rot

The most dreaded onion disease of them all.

Symptoms: fluffy white fungus on roots with tiny black specks (sclerotia). Once it’s in the soil, it can survive 15+ years.

Step-by-step prevention:

1. Rotate out of alliums (onions, garlic, leeks) for at least 7–8 years.

2. Solarize soil in summer by covering with clear plastic to bake the fungus.

3. Remove and destroy all infected plants immediately.

Faith Tie-In: White rot is a long-game battle. It reminds me of James 5:7: “See how the farmer waits for the precious fruit of the earth, waiting patiently for it until it receives the early and latter rain.” Stewardship sometimes means playing the long game.

Region-Specific Advice

• Zone 3–5: Focus on curing and storage. Cool, damp cellars invite rot if onions aren’t fully dried.

• Zone 6–9: Watch for soilborne issues—rotate longer and keep soil light.

• Zone 10+: Heat-tolerant varieties and drip irrigation are essential. Fungus pressure rises fast with high humidity.

Printable Tool

👉 Download the Onion Disease Prevention Checklist — a one-page guide covering spacing, rotation schedules, curing steps, and storage temperatures. Pin it in your shed or tape it to your cellar door for quick reference.

Closing: Protecting Your Harvest

Onions will humble you if you take them for granted, but they’ll reward you if you give them what they need. Stay ahead of these five diseases with a little planning, and you’ll have a pantry full of crisp, sweet bulbs that last you through the winter.

Take a moment this week to review your onion plan. Mark your crop rotation, set up your curing area, and make a note of storage temperatures. You’ll thank yourself when the snow flies and you’re still pulling good onions from the bin.