How to Prune and Deadhead Echinacea (Coneflower) to Prevent Aster Yellows

Coneflowers (Echinacea), with their vibrant blooms and pollinator appeal, are a staple in many home gardens. In this post, I’ll share my approach to pruning coneflowers to encourage healthy blooms, support pollinators, and provide food for birds later in the season. I’ll also cover a serious plant disease—aster yellows—that can affect coneflowers and other members of the aster family, and how to deal with it effectively.

When to Prune Coneflowers

My general philosophy is to prune coneflowers during the growing season when there’s still plenty of time for them to produce new blooms and seeds before frost.
Here in Tennessee, that usually means I am pruning once in mid to late summer. You can deadhead as you go as well through the early summer but give your plants their final pruning and deadheading with 4-6 weeks before the first frosts come to give them plenty of time to produce seed.

For example, in early August, we still have enough time before our average mid-October frost for the plants to put on new flowers and set seed. Those seeds are important food for goldfinches and other birds in fall and winter.

Pruning at this stage ensures:

• Pollinators still have fresh blooms to feed on through summer.
• Birds have seeds in fall and winter.
• Plants maintain a tidier, more upright appearance.

While seeds are great for wildlife, during the active growing season I focus on keeping blooms coming for the pollinators—bees, butterflies, and even migrating monarchs. Fresh flowers give them the nectar they need to fuel their journeys or prepare for overwintering. During the growing season the birds have access to a number of food sources like insects and can get plenty to eat. In the late fall and winter these food sources dwindel so having echinacea at the right time can help them out.

Quick-Reference Pruning Guide

When to Prune	How to Prune	Why Prune
Mid to late summer, while enough time remains before frost	Cut stems back to just above a set of healthy leaves	Encourage more blooms for pollinators, produce seeds later for birds

How to Deadhead and Prune Coneflowers

When pruning, look at each stem individually and identify its stage:

1. Fully Seeded Flower Heads
   If the flower head is fully brown and dry, seeds are ready for birds. I often harvest these and place them in areas where goldfinches can easily find them.
2. Spent Blooms Beginning to Seed
   These can be cut back to encourage more blooms. I typically trim the stem just above a pair of healthy leaves so the plant can produce new branches and flowers from that point.
3. Healthy Blooms
   Leave these for the pollinators.

If a plant is flopping over or crowding other plants, I cut it back more aggressively—sometimes by half its height—to open space and encourage new, upright growth. For example, I had a tall coneflower shading a coreopsis plant underneath. Unfortunately, I waited too long to prune and the coreopsis crown rotted, so timely pruning is important if coneflowers are overshadowing neighbors.

Understanding Aster Yellows

While pruning, I noticed a disease affecting some of my plants: aster yellows.
This is caused by a microscopic organism called a phytoplasma and is spread from plant to plant by leafhoppers which area tiny insects that feed on plant sap.

Symptoms of aster yellows include:

• Distorted, leafy growth emerging from flower centers
• Flowers turning an unusual green color
• Deformed petals and abnormal seed heads

Unfortunately, there is no cure. Infected plants must be removed entirely to prevent spread to other coneflowers and members of the aster family (such as black-eyed Susans, daisies, and sunflowers). Aster yellows will persist in wild plants outside of your garden as well so it is very tough to eliminate.

How to Remove Infected Plants

When I find an infected plant:

1. Trace the stem to the base to confirm which crown it belongs to.
2. Pull the entire plant out, roots and all.
3. Dispose of it in the trash—not the compost pile—to avoid reintroducing the disease.

The good news? Aster yellows does not survive in seeds, so if your infected plant has produced seed, you can safely save and plant it for healthy new growth next year. Aster yellows also does not persist in the soil but I prefer not to take chances with the compost.

Preventing Spread Without Harming Pollinators

While some gardeners might be tempted to use insecticides to control leafhoppers, sprays can harm beneficial insects like bees and butterflies. (Coneflowers are the larval food source for the silvery checkspot butterfly) I avoid chemical controls for this reason and focus on monitoring plants regularly and removing infected ones as soon as I spot them.

I also avoid planting too many high-value hybrids of coneflowers in one spot, as dense plantings can make disease spread more likely. I love some of the colors they have created but those hybrid coneflowers are expensive to replace so growing coneflowers from seed is easy and a whole lot less expensive!

See more on Pruning Echincea and Aster Yellows in the video Below

Saving Coneflower Seeds

Since seeds are safe to use even from infected plants, here’s how I save them:

1. Wait until seed heads turn completely brown and dry.
2. Snip them into a paper bag.
3. Store in a cool, dry place until planting.

Bonus tip: Leave some seed heads standing for winter interest and to feed birds naturally.

Here is more on Saving Coneflowers from Seed.

After Pruning: Garden Opportunities

Once the coneflowers are pruned, you might notice:

• More airflow between plants, which helps reduce disease risk.
• Open spaces for planting fall annuals or cool-season flowers.
• Opportunities to transplant self-seeded coneflower seedlings from other parts of the garden.

Wildlife in the Coneflower Patch

Coneflowers are more than just garden beauty—they’re a seasonal hub for wildlife.

Visitors I often see include:

• Goldfinches eating seeds in late summer/fall.
• Monarch butterflies stopping for nectar during migration.
• Native bees gathering pollen and nectar all summer.

By timing pruning correctly, you can serve both pollinators and seed-eating birds in the same season.

Final Thoughts

Gardening always comes with challenges – whether pests, diseases, or weather. With coneflowers, pruning at the right time keeps blooms coming, supports pollinators, and provides seed for birds later in the season. And while aster yellows can be frustrating, removing affected plants quickly can protect the rest of your garden.

Have you dealt with aster yellows in your garden? Share your experiences in the comments below – I’d love to hear your tips.