Imagine peeling an onion, expecting the crisp freshness beneath its papery skin, only to discover stubborn black patches staring back at you. At first glance, these marks might seem like dirt or damage, but they tell a different story, one of a persistent fungus thriving quietly in the shadows of storage rooms.
The black patches seen on onions are not dirt but caused by a fungus known as Aspergillus niger. This fungus thrives in warm, humid, and poorly ventilated storage environments, leading to spoilage and significant losses in onion crops in India.
According to scientific studies, it may produce harmful toxins, making it essential to buy fresh onions, store them properly in well-ventilated bags, peel spoiled parts, or discard affected onions. Experts recommend learning to choose healthy onions and adopting best storage practices to minimise health risks.
What Are These Black Patches?
The dark spots you see on onions are not dirt or bruises. They are actually black mold, a fungus called Aspergillus niger. This mold grows on the outer layers of onions during storage, especially when conditions are warm, wet, and poorly ventilated. It starts as tiny white spots that gradually turn dark brown or black over time.
Why Do Onions Get These Black Patches?
Black mold loves three things: warmth, moisture, and poor air circulation. When onions are stored in hot, humid rooms without proper ventilation, the fungus thrives and spreads quickly. A 2020 scientific study found that 98% of onion samples from Indian markets contained this black mold fungus, showing how common this problem is.
The fungus is naturally present in soil, so onions pick it up during farming. However, it only becomes visible and harmful when storage conditions are unfavorable.
Are They Harmful to Your Health?
The answer is not straightforward. Some strains of black mold can produce harmful chemicals called mycotoxins. These are poisons that can damage your kidneys, liver, and immune system if consumed in large amounts. However, not all black mold produces these harmful chemicals.
The risk depends on several factors:
- How much mold is present
- Which type of mold strain it is
- Your own health status
Scientific studies have shown that some Aspergillus niger strains can produce mycotoxins like ochratoxin A and fumonisin B2, toxins linked to health risks ranging from immune suppression to kidney damage and carcinogenicity (PMC, 2020).
Additionally, medical literature highlights the potential of Aspergillus niger to cause infections, especially in immunocompromised individuals, through airborne spores or handling contaminated produce (Journal of Advanced Microbiology Research, 2024).
Although the presence of black patches does not guarantee toxin production, consumption of heavily moldy onions is not advised due to potential health hazards. You may still use it by peeling off the layer with black patches and rinse the onion properly, if only dry outer layers are affected. If inner fleshy layers show mold, soft spots, or musty smell: discard entirely.
Understanding Aspergillus niger on Onions
Aspergillus niger is a black mold fungus widely found on onions, especially during storage. A 2020 molecular study published in PMC revealed that Aspergillus section Nigri strains, including A. niger and its close relative A. welwitschiae, were isolated from 98% of onion samples tested, confirming the high prevalence of these fungi on Indian onions (PMC, 2020).
The fungus flourishes particularly in warm and humid conditions where airflow is minimal, such as poorly ventilated storerooms. Early growth starts as white patches that turn into distinctive black fungal colonies, leading to onion rot (Plant Pathology Journal, 2023).
How to Stay Safe
Best approach: Simply throw away onions with large black patches. This is the safest option.
If patches are minor: You can peel away the outer dark layers and discard them completely. Then wash the remaining onion under running water before cooking.
Prevention is key:
- Keep storage temperature between 25-30°C with 60-70% humidity
- Buy fresh onions from clean shops
- Store onions in cool, dry places with good air flow
- Keep onions in breathable bags, not sealed containers
- Store onions and potatoes separately (potatoes release moisture that causes onions to spoil)
Scientific Recommendations, Emerging Solutions
Agricultural researchers advocate using cold storages, maintaining proper airflow, and integrating natural antifungal treatments. A 2019 study in Postharvest Biology and Technology found that essential oils extracted from citrus peels effectively reduced Aspergillus niger biofilm formation on onions, suggesting promising eco-friendly control measures.
Additionally, fungicide treatments like dinocap have shown efficacy under controlled conditions to inhibit fungal growth on onions (IJCMAS, 2017). However, these methods require careful application due to safety concerns, highlighting the importance of preventive storage techniques at the consumer and farmer levels.
Disclaimer: This article is for informational purposes only and does not substitute for professional medical advice. Always consult a healthcare professional if you experience health issues related to food consumption.

