What you see: Distinct black spots on your basil.
What it is: Likely the work of a hungry microbe.
Eat or toss: Leaves with black spots, eeeehhh… I’m tossing those. Other leaves that still look normal should be fine.
Basil is notoriously finicky (see our deep dive on what refrigeration temperatures do to it here). When we see discolored areas on our store-bought basil, chilling injury is the most likely culprit. That often shows up as grayish or brownish patches that spread and deepen to black over time.
But what if you’re seeing discrete black spots, like on this basil? We can’t totally rule out chilling injury, but spots like these are more likely to be the work of a microbe. Chilling injury tends to show up in the parts of the leaves in between the veins, but see how, in the image, the spots straddle some of the leaves’ veins? And how the spots have more defined borders than the patchy graying and browning of chilling injury? See that sort of bullseye at the center of each black spot? These symptoms point toward some kind of disease.
While we can never be 100% certain when assessing an image of an afflicted plant, Arlan James Rodeo, an assistant Professor at the University of the Philippines Los Baños who specializes in basil, said that from looking the image he would guess it’s “more like a bacterial disease than a fungi because of the irregular leaf spots with a gray/brown center. Usually, fungal diseases in basil starts with yellowing and then browning, spreading outward from the middle. This will also have a fuzzy texture on the underside as the fungus develops reproductive structures.”
Ok, so if it’s a microbe’s doing, should you eat or toss? I’m on team “toss.” Microbes alter the chemistry of food with the substances they generate and excrete as they break things down—the basil might not taste great. In addition, a weakened plant could also be hosting a wider array of microbes and you’d have no idea what you might inadvertently consume (to be fair, the surfaces of any uncooked fruits and vegetables, even those that look pristine, sport an array of microbes and are not risk free. For most of us, however, the health benefits of fresh fruits and vegetables that aren’t sporting evidence of infection outweigh that slight risk).
Eating an occasional spotty leaf like this is unlikely to result in an acute illness. But, it’s certainly marginally riskier than a leaf without such signs of disease. And, ultimately, this basil leaf may not taste very good anyway.
SOURCES:
- Arlan James Rodeo, Ph.D., Assistant Professor at University of the Philippines Los Baños. Ph.D. research at University of California – Davis. Interview over email September and October 2025.
- Gray Patches on Basil. R. Jackson. EatOrToss. November 2025.
- Rodeo AJD, Mitcham EJ. Chilling temperatures and controlled atmospheres alter key volatile compounds implicated in basil aroma and flavor. Front Plant Sci. 2023 Jul 3;14:1218734.


