Is Bat Guano Safe to Use in the Garden?

Bat guano is an amazing organic fertilizer, but it may pose risks to humans, plants, and bat colonies. Former organic farmer Logan Hailey digs into the science and nuances of safely using bat guano in your garden.

Two rust and black fruit bats hang from the branches of a tree in the garden.


We gardeners are always looking for natural sources of pest control and fertility to help our gardens thrive. Bat guano has gained much popularity as an organic fertilizer thanks to its potent nitrogen and phosphorus concentration. But is it safe?

This natural resource has many safety and ethical concerns to consider before adding it to your garden beds. We must consider the endangerment of bats, how guano could potentially harm human health, and why you might want to avoid store-bought guano fertilizer and opt for personal bat boxes instead.

Let’s dig into everything you need to know about using bat guano in your garden without harming yourself, your plants, or the ecosystem as a whole.

What is Bat Guano?

Close-up of Bat dung, guano, poop, droppings, feces, and excrement on the ground. It looks like a dry, crumbly substance of brown-black color.
This potent organic fertilizer is high in nitrogen and phosphorus and boosts plant growth.

Bat guano is a nutrient-rich manure harvested from insectivorous and fruit-eating bats. This excrement is an organic fertilizer because it is particularly high in readily available nitrogen and phosphorus, helping plants grow stronger and greener to produce higher yields.

Unlike chicken or cow manure, guano is low-odor, fast-acting, and safe to apply directly to plants without as much risk of fertilizer burn.

The Short Answer: Bat Guano is Safe When Handled Like Any Other Manure

The prevailing expert opinion is that bat guano is safe for humans and garden plants but may not be ecologically “safe” for bats themselves. Like most manures, you should take basic precautions when handling guano. Gloves and proper sanitation are essential to prevent the spread of pathogens. Whether you are applying store-bought fertilizer or collecting guano from beneath your own bat boxes (more on this below), it is essential to thoroughly wash your hands and avoid eating or drinking while handling it. After all, it’s still poop!

The Long Answer: There are Nuances to Safe and Ethical Use in The Garden

The safety of products used in our homes and gardens is often far more nuanced than a label like “safe” or “dangerous.” Some pesticides were considered safe according to government regulation in the 1960s but later became outlawed due to new science that they cause cancer or birth defects.

Some plants are considered safe to handle but may cause rashes or problems for individuals with certain health conditions. Certain garden inputs are safe for humans but may harm bees and butterflies. 

Safety occurs on a spectrum and requires zooming out to see the big picture of how our decisions affect us, our gardens, and the world around us. To understand how bat guano fits in this picture, let’s examine its safety from three angles:

  1. Human Safety
  2. Plant Safety
  3. Environmental (Bat) Safety

It’s (Mostly) Safe for Humans

lose-up of a man's hand holding bat guano organic fertilizer over a fertilizer bag. Organic fertilizer bat guano is a natural and nutrient-rich plant amendment derived from the accumulated droppings of bats. It presents as a granular or powdery substance with a dark brown to black color
Bats, often misunderstood, pose minimal safety risks. The use of their droppings is safe with precautions.

While many people associate bats with vampires and rabies, these nocturnal mammals don’t pose much risk to human safety. In fact, they can help prevent many human diseases by devouring thousands of mosquitoes per night, including those that harbor the West Nile virus.

When it comes to handling bat guano in the garden, the safety risks are about the same as spreading chicken manure or handling dog poop. Of course, all forms of animal excrement contain potentially harmful pathogens, but as long as you wear gloves and thoroughly wash your hands, they are unlikely to cause major health problems.

Key Caveat for Dried Guano: You may consider wearing a mask when applying dried guano due to the potential contamination with the spores of a fungus called Histoplasma capsulatum, often found in the dust of dry bat manure. If inhaled, these spores could cause a serious human respiratory disease called histoplasmosis. However, bat experts assert that this disease is very rare, and the risk of transmission through guano is very low. Still, it’s best to do your own research and prevent contamination in a way that feels right for you.

In my humble opinion, as a novice bat researcher and an experienced organic farmer/gardener, I avoid buying dried guano altogether. I don’t want to risk my lungs or contribute to declining bat populations.

Instead, I recommend collecting the droppings that fall naturally below eco-friendly bat boxes you can build in your garden. You get free manure fertilizer and natural pest control without the safety or ethical concerns associated with store-bought guano fertilizer!

It’s Safe for Plants

Close-up of organic fertilizer bat guano in spoon over young strawberry seedlings in black planting bags. Strawberry seedlings exhibit a distinctive appearance characterized by small, serrated, and tri-foliate leaves arranged in clusters on delicate stems.
Like worm castings, bat droppings are a gentle and safe plant fertilizer.

This manure-based fertilizer is especially popular thanks to its safety for garden crops. Due to the unique nutrient composition of bat guano, it is mild on plants and unlikely to cause fertilizer burn.

It is similar to worm castings because it can be applied directly to the garden. Guano is gentle on your crops, unlike chicken or cow manure, even if you don’t compost it first. It is rich in microorganisms that make the nutrients readily available to plants. 

However, a little goes a long way! The low application rate of guano is another benefit to the plant. To increase plant growth, you only need about 1 part guano to 20 parts soil. No need to dump it on!

Questionable Safety for Bats 

Close-up of a fruit bat is hanging upside down on a blurred background. Fruit bats, also known as flying foxes, are characterized by their distinct appearance, combining features of both bats and mammals. They have large eyes, fox-like faces, and elongated snouts. Their wingspan has a leathery wing membrane.
Commercially harvested guano poses risks, spreading White Nose Syndrome and endangering bat populations.

When considering the safety of this fertilizer for bats themselves, things get a bit more complex. When the droppings are commercially harvested for fertilizer, collectors enter many caves to collect them. In the process, they may spread a deadly fungal disease called White Nose Syndrome between bat colonies. Fertilizer collection is the primary reason for contamination of caves, leading to major risks for wild bat populations. 

Although this pathogen is transmitted from bat to bat, the U.S. Geological Survey highlights that humans inadvertently contribute to faster spread because the disease-causing spores attach to their clothing gear. Note that these fungal spores differ from those that cause human respiratory illness. However, it’s pretty interesting (and sad) that guano fertilizer harvesting poses health risks to humans and bats! 

The story’s moral is that if you care about saving bats, don’t buy store-bought guano. You don’t know how it is being harvested, and it likely isn’t safe for endangered bats.

What’s the Problem?

The main problems come from two angles: environmental ethics and human health.

Environmental Ethics

Close-up of Horseshoe bats hanging in a cave. Their medium-sized bodies are covered in fur that varies in color, ranging from brown to gray. They have dark brown, large, membranous wings.
Bat guano faces environmental and health challenges despite its benefits, impacting bat populations worldwide.

While bat poop is tremendously beneficial in gardens and on farms, it poses some environmental and health safety challenges. Bats are facing widespread decimation worldwide, with more than half of the bat species in the U.S. listed as severely threatened or endangered

The causes for bat declines are multifaceted, including pressures like:

  • Climate change
  • Habitat destruction
  • Pollution
  • Lack of food (when pesticides and chemicals kill their insect food sources)
  • Pesticide bioaccumulation (when bats eat a lot of insects sprayed with pesticides, they are exposed to increasingly high levels of toxins)
  • Hunting and poaching
  • White Nose Syndrome (a fungal disease that disrupts bat’s natural hibernation cycles)
  • Commercial harvesting

Those last two bullet points are the most problematic for gardeners because our fertilizer could come from unethical sources. You may wonder how collecting an animal’s poop could harm them. The issue is not related to the poop collection itself but the fungus that may spread via the clothes, shoes, and tools of commercial guano harvesters.

White Nose Syndrome and Fertilizer Harvesting

Top view, close-up of a glass bowl full of Bat manure on a white table with green leaves. Bat manure is in the form of round, black granules.
A lethal bat disease, White Nose Syndrome spreads through commercial guano harvesting, endangering bat populations.

White Nose Syndrome is a severe fungal disease that is killing bats worldwide. It is the most dire threat to bats because it spreads rapidly from bat to bat and severely disrupts their hibernation cycles, causing them to awaken in the middle of the winter, fly out of their caves, and starve or freeze to death. 

How does that relate to gardening? Commercial harvesting is a key cause of the spread of White Nose Syndrome. When humans enter caves to collect the poop to sell as fertilizer, they can inadvertently spread the fungus from cave to cave, causing more and more bats to get infected. Much like a super contagious human disease, when one member of a colony (family) of bats is exposed to the fungus, it rapidly spreads to the rest.

Unfortunately, sanitation measures and guidelines have still been unsuccessful at slowing this spread. If we want to use this fertilizer in the garden ethically, the best choice is to install our own bat boxes and collect the guano from beneath them, much like you would from your chicken coop.

Human Safety Issues

Close-up of a man's hands holding a bat in a cave. Bats are mammals with elongated fingers covered by a thin membrane of skin, forming wings that allow for flight. The body size of the bat is small, mouse-sized, covered entirely in grey-brown hairs and has large ears.
Histoplasmosis is a concern during cleanup.

A serious respiratory disease called histoplasmosis is another key concern when handling and using guano in the garden. The microscopic spores of a fungus called Histoplasma capsulatum are sometimes found in dried bat guano and can harm humans if inhaled. This rare disease most commonly occurs when people breathe in these spores while demolishing or cleaning up attics and houses where bats have overwintered. 

Interestingly, fresh bat droppings do not pose the same risk. This dangerous fungus prefers dried, aged guano. In addition to the ethical issues mentioned above, this key safety concern can be mitigated by building bat boxes near your garden and collecting guano yourself rather than buying it.

Collecting from Bat Boxes

Close-up of bat houses hanging from a tree branch against the blue sky. A bat house is a wooden structure designed to provide a roosting habitat for bats. These houses are rectangular, featuring multiple chambers with internal partitions that mimic the crevices found in natural roosting spots such as tree bark or rock crevices. This bat house has a black engraving of the bat outline.
Install bat boxes for pest control and collect guano for an ethical, abundant garden fertilizer.

Bat boxes are an emerging trend that offers amazing benefits for gardeners and bats! Official state governments even have conservation projects to promote building bat boxes to aid in ecological health. Bats are some of the best pest-control agents you can have in your garden. Installing a bat box in your yard can help protect these threatened mammals while enjoying reduced insect pest pressure for your plants. 

U.S.-native brown bats are particularly voracious predators of mosquitoes, cucumber beetles, and moths. When bats eat night-fluttering moths, they can dramatically reduce infestations of pests like cabbage loopers, tomato hornworms, and army cutworms, all of which are larval stages of adult moths.

Better yet, you can use the droppings that accumulate under a bat box as fresh fertilizer in your garden! Much like roosting chickens, bats sleep on elevated stands inside bat houses. The bottom of a bat box is open so the poop won’t accumulate inside. 

While they sleep, their guano drops to the ground and can be collected by placing a bucket, saucer, or potted plant underneath the bat box. Suddenly, you have a free, abundant, and ethical supply to use in your garden! Installing bat boxes and using the guano from local bats is a far safer, eco-conscious option for this nutrient-rich fertilizer

Remember that bats sleep during the day, so it’s important not to disturb the box. This shouldn’t be an issue if your bat box is installed at the recommended 20 feet or higher above the ground. As we mentioned above, take care to handle the bat droppings just like you would handle any poop— with obvious sanitation measures! 

Final Thoughts

Bat guano is safe for humans and plants, but store-bought guano may be risky for threatened wild bats. Using this fertilizer is nuanced, but the material is safe if you use sanitation precautions. If you want to help protect threatened bats and slow the spread of White Nose Syndrome, avoid buying store-bought guano fertilizer. Instead, encourage them to visit your garden and install bat boxes! You can collect guano from beneath the box and also enjoy the major pest-prevention benefits of local bat populations.

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