What causes brown spots in tomatoes?

Brown spots in tomatoes are a very common and frustrating issue for gardeners, most frequently caused by a physiological disorder called blossom end rot (BER) on the fruit, or various fungal and bacterial diseases on the leaves and stems. Other culprits include environmental stressors like sunscald, cold damage, or inconsistent watering, and occasionally pest damage. Identifying the specific appearance and location of the brown spots is crucial for accurate diagnosis and effective treatment.

What are the most common brown spots on tomato fruit?

When you see brown spots on tomato fruit, the vast majority of the time it points to one primary culprit: Blossom End Rot (BER). While other issues can cause discoloration, BER is uniquely prevalent and easily recognizable on the fruit itself. Understanding its appearance and cause is essential for any tomato gardener.

Here are the most common brown spots found on tomato fruit:

Blossom End Rot (BER) - The #1 Cause:
- Appearance: This is the classic brown spot on tomato fruit. It begins as a small, watery, discolored spot on the bottom (blossom end) of the tomato, opposite the stem. As it progresses, the spot enlarges, turns dark brown or black, becomes sunken and leathery, and often looks flattened or somewhat squishy. It can affect green or ripening fruit.
- Cause: Blossom end rot is a physiological disorder, not a disease caused by a pathogen. It results from a calcium deficiency in the developing fruit, which occurs due to inconsistent water delivery to the plant, rapid growth spurts, root damage, or sometimes extreme fluctuations in soil moisture (too wet then too dry). It is rarely due to a lack of calcium in the soil itself, but rather the plant's inability to transport it to the fruit efficiently.
- Impact: Renders the affected part of the fruit inedible and can destroy entire harvests if not addressed.
- Solution: Focus on consistent and adequate watering. Apply mulch around plants to regulate soil moisture. Avoid over-fertilizing with high nitrogen. Ensure proper soil pH (6.0-6.8). Do not add calcium to the soil unless a soil test confirms a deficiency, as it can worsen the problem by locking out other nutrients if pH is raised. Foliar calcium sprays offer temporary, limited help. Gardener's Best Organic Mulch
Sunscald:
- Appearance: Sunscald appears as a light-colored (white or yellowish) blistered area on the shoulders or sides of green or ripening fruit that are directly exposed to intense sunlight, especially during hot weather. As the damage progresses, the blistered area becomes papery, turns grayish-brown or black, and often becomes sunken. It's often on the uppermost, most exposed fruits.
- Cause: Direct, intense sunlight (solar radiation) combined with high temperatures. It's essentially a plant sunburn. It's common after heavy pruning that suddenly exposes fruit, or on varieties with sparse foliage.
- Impact: Renders the affected part of the fruit unappetizing and susceptible to secondary fungal or bacterial infections.
- Solution: Ensure good foliage cover by avoiding over-pruning. Choose disease-resistant varieties that maintain dense foliage. Consider using shade cloth over plants during extreme heat waves (temperatures consistently above 90°F / 32°C).
Late Blight (Fungal - Serious!):
- Appearance: This is a devastating fungal disease. On fruit, it starts as greasy-looking, dark brown to black lesions that can quickly spread, covering large areas. These spots are typically firm and sunken and can appear on any part of the fruit, not just the blossom end. Often, a white, fuzzy fungal growth might be visible on the edges of lesions, especially in humid conditions. It also severely affects leaves and stems.
- Cause: Caused by the water mold Phytophthora infestans. It spreads rapidly in cool, wet, humid conditions.
- Impact: Can destroy entire tomato crops very quickly.
- Solution: This is a severe disease. Remove and destroy (do not compost) infected plants immediately. Improve air circulation. Avoid overhead watering. Use preventative fungicides in susceptible areas. Plant resistant varieties.
Bacterial Speck / Bacterial Spot:
- Appearance: These are bacterial diseases. On fruit, they cause tiny, raised, dark spots that can be surrounded by a narrow, light green halo. The spots are typically small (1/16-1/8 inch), superficial, and the fruit usually remains edible by cutting them off.
- Cause: Bacterial pathogens (Pseudomonas syringae pv. tomato for speck, Xanthomonas campestris pv. vesicatoria for spot). Spread by splashing water, rain, and tools.
- Impact: Primarily aesthetic damage to fruit; severe infections can lead to leaf yellowing and drop, weakening the plant.
- Solution: Practice good garden sanitation. Avoid overhead watering. Use certified disease-free seeds/plants. Rotate crops. Copper-based sprays can be used protectively.

When diagnosing brown spots on your tomato fruit, always note the location (blossom end vs. exposed side), texture (mushy/leathery vs. papery/crispy vs. firm), and whether the spots are accompanied by other symptoms on leaves or stems.

What diseases cause brown spots on tomato leaves and stems?

Brown spots on tomato leaves and stems are very common and are usually signs of various fungal or bacterial diseases. These pathogens thrive in specific environmental conditions and can quickly spread, significantly impacting plant health and fruit production. Accurate identification is key to effective management.

Here are the primary diseases that cause brown spots on tomato leaves and stems:

Early Blight (Alternaria solani):
- Description: One of the most common fungal diseases. Appears as dark brown to black spots with concentric rings (like a target pattern) on older, lower leaves and stems first. Surrounding tissue often turns yellow. Lesions on stems can be sunken.
- Cause: A fungus that overwinters in soil and plant debris. Favored by warm, humid conditions with splashing water.
- Impact: Leads to premature defoliation (leaves drop off), exposing fruit to sunscald and reducing yield.
- Solution:
  1. Sanitation: Remove and destroy infected lower leaves immediately. Clean up all plant debris at the end of the season.
  2. Mulch: Apply mulch around plants to prevent soil splash.
  3. Air Circulation: Ensure good air circulation by proper spacing and pruning lower leaves.
  4. Water at Base: Avoid overhead watering.
  5. Fungicides: Copper-based or organic fungicides like Bonide Copper Fungicide Bonide Copper Fungicide can be used preventatively or at early signs.
  6. Resistant Varieties: Plant resistant varieties.
Late Blight (Phytophthora infestans):
- Description: A highly aggressive fungal disease (water mold). On leaves, it causes large, irregular, dark brown to black, water-soaked lesions that rapidly expand. A white, fuzzy fungal growth may be visible on the undersides of leaves, especially in humid conditions. Stems also develop large, dark lesions.
- Cause: The same pathogen that caused the Irish potato famine. Spreads rapidly by wind and splashing water in cool, wet, humid conditions.
- Impact: Can quickly kill entire plants and destroy whole crops within days.
- Solution:
  1. Immediate Removal: Destroy (do not compost) infected plants and fruit as soon as possible.
  2. Sanitation: Remove all tomato/potato debris at season end.
  3. Prevention: Plant resistant varieties. Apply preventative fungicides (e.g., copper or chlorothalonil-based) in high-risk areas. Improve air circulation.
Septoria Leaf Spot (Septoria lycopersici):
- Description: A very common fungal disease. Causes numerous small, circular brown spots (1/8 to 1/4 inch) on older, lower leaves. Each spot typically has a distinctive dark brown border and a tan or gray center with tiny black dots (pycnidia - fungal fruiting bodies) in the middle. Affected leaves often turn yellow and fall off prematurely.
- Cause: A fungus that overwinters in plant debris. Spreads by splashing water and wind. Favored by high humidity and moderate temperatures.
- Impact: Leads to defoliation, stressing the plant and reducing fruit size/quality.
- Solution: Similar to Early Blight: sanitation, mulching, watering at the base, improving air circulation. Fungicides (copper or Daconil) can be used.
Bacterial Spot and Bacterial Speck (Xanthomonas campestris pv. vesicatoria & Pseudomonas syringae pv. tomato):
- Description: Bacterial diseases. On leaves, they cause small, angular to irregular, dark brown or black spots.
  - Bacterial Spot: Spots may be water-soaked, greasy, and larger.
  - Bacterial Speck: Spots are typically smaller, raised, and might have a slight yellow halo.
  - Affected areas may merge, and severe infections can cause yellowing and leaf drop.
- Cause: Bacteria spread by splashing water, rain, and contaminated tools/seeds. Favored by warm, wet, humid conditions.
- Impact: Reduces plant vigor and yield; fruit also gets spots.
- Solution:
  1. Sanitation: Crucial. Remove infected leaves/stems. Clean up all plant debris.
  2. Avoid Overhead Watering: Water at the base.
  3. Crop Rotation: Rotate tomatoes to a new spot each year.
  4. Certified Seeds/Plants: Use only disease-free seeds or plants.
  5. Copper Sprays: Copper-based bactericides can offer some preventative protection.
Fusarium Wilt (Fusarium oxysporum f. sp. lycopersici) & Verticillium Wilt (Verticillium albo-atrum):
- Description: These are soil-borne fungal diseases that affect the plant's vascular (water transport) system.
- Symptoms: Initially, lower leaves turn yellow, often starting on one side of the plant or a single branch. The yellowing progresses to brown, followed by wilting (especially on hot days) and eventual death of the affected stem or the entire plant. If you cut open an infected stem, the vascular tissue might be discolored (brown streaks).
- Cause: Fungi enter through roots and clog water-conducting tissues. Can persist in soil for years.
- Impact: Lethal. Leads to rapid plant death.
- Solution: No cure.
  1. Resistant Varieties: Crucially, plant tomato varieties labeled "F" (Fusarium) or "V" (Verticillium) resistant. This is the best defense.
  2. Crop Rotation: Do not plant tomatoes or other susceptible plants in affected soil for 3-5 years.
  3. Sanitation: Remove and destroy infected plants.

General Preventative Measures against Tomato Diseases:

Choose Resistant Varieties (always check labels!): This is your strongest defense against many common diseases.
Rotate Crops: Don't plant tomatoes in the same spot year after year.
Good Air Circulation: Space plants adequately and prune lower leaves.
Water at the Base: Avoid overhead watering.
Sanitation: Keep garden beds clean of plant debris.
Certified Disease-Free Plants/Seeds: Start with healthy stock.

By diligently scouting for these distinct types of brown spots and implementing appropriate preventative and treatment strategies, you can protect your tomato plants from debilitating diseases.

What environmental factors cause brown spots on tomato leaves and stems?

Beyond specific diseases, various environmental factors can directly cause brown spots on tomato leaves and stems by stressing the plant, leading to tissue damage or compromising its ability to grow optimally. These stressors often mimic disease symptoms but are purely physiological.

Here’s how different environmental factors can cause brown spots:

Sunscald / Heat Stress:
- Problem: Intense, direct sunlight, especially during hot summer days, can be too much for tender tomato leaves, similar to sunburn on fruit.
- Impact: Leads to localized tissue death on exposed leaves, appearing as bleached white or yellow spots that quickly turn crispy brown or black. This is often seen on upper leaves directly exposed to the sun, especially if pruning has removed protective foliage too aggressively.
- Symptoms: Crispy brown/black patches on leaves, often concentrated on the sunny side of the plant. May also affect stems.
- Solution:
  1. Avoid Over-Pruning: Allow enough foliage to remain to shade developing fruit and protect lower leaves.
  2. Provide Temporary Shade: During extreme heat waves (consistently above 90°F / 32°C), consider using shade cloth (30-50% shade) over your plants during the hottest part of the day.
  3. Adequate Watering: Ensure consistent soil moisture, as water-stressed plants are more susceptible to sunscald.
Inconsistent Watering (Leading to Root Stress and Nutrient Problems):
- Problem: Erratic watering – periods of extreme dryness followed by heavy watering, or consistently waterlogged soil – severely stresses tomato roots.
- Impact:
  - Root Damage/Rot: Overwatering leads to root rot (roots turn brown/black and mushy), preventing water and nutrient absorption. This causes wilting and leaves eventually turn yellow then brown and crispy due to dehydration.
  - Dehydration: Chronic underwatering causes cells to collapse, leading to crispy brown edges and tips, eventually browning entire leaves.
- Symptoms:
  - Mushy brown spots on leaves/stems, wilting with wet soil: Points to overwatering/root rot.
  - Crispy brown edges/tips on leaves, dry soil, wilting: Points to underwatering.
- Solution:
  1. Consistent Watering: Water deeply and regularly, especially during dry spells. Use drip irrigation or a soaker hose for consistent moisture. Rain Bird Drip Irrigation Kit
  2. Mulch: Apply a thick layer of mulch (straw, wood chips) around plants to regulate soil moisture and temperature.
  3. Ensure Drainage: Plant in well-draining soil.
Cold Damage / Chilling Injury:
- Problem: Tomatoes are warm-season plants. Temperatures below 50-55°F (10-13°C) can cause chilling injury, and temperatures at or below 32°F (0°C) cause frost damage.
- Impact: Cold temperatures damage cell membranes. Leaves will turn yellowish, then black or dark brown, and often become limp and water-soaked initially, then crispy. This is especially true for tender new growth after a spring frost, or older foliage in an early fall cold snap. Stems can also show dark lesions.
- Symptoms: Widespread black or dark brown, mushy or crispy patches, particularly on exposed leaves.
- Solution:
  1. Protect from Frost: Cover plants with row covers or old sheets if frost is predicted.
  2. Plant at Right Time: Don't plant tomatoes out too early in spring.
  3. Choose Hardy Varieties: Some tomato varieties are slightly more cold-tolerant than others.
Nutrient Excess (Fertilizer Burn / Salt Buildup):
- Problem: Over-fertilizing, especially with synthetic fertilizers that are high in salts, or allowing salts to build up in the soil (common in containers or from hard water).
- Impact: High salt concentrations can draw water out of the plant's roots, leading to root burn. This causes the leaf margins and tips to turn crispy brown, often with a yellow halo. It mimics dehydration or root rot.
- Symptoms: Crispy brown edges/tips, especially on older leaves. White crust on soil surface or pot rim.
- Solution:
  1. Dilute Fertilizer: Always dilute liquid fertilizers to half or quarter strength, especially in hot weather.
  2. Water Before Fertilizing: Always water plants thoroughly before applying granular fertilizer.
  3. Flush Soil: Periodically, leach the soil by watering thoroughly with plain water until a large volume drains out, to wash away accumulated salts.

By carefully observing your tomato plants and their environment, you can often pinpoint the specific environmental stressor causing brown spots and apply the appropriate corrective measures.

Can physical damage or pests cause brown spots in tomatoes?

Yes, beyond diseases and environmental stressors, physical damage and pest infestations can also lead to brown spots in tomatoes. These issues directly injure plant tissues or weaken the plant significantly, causing localized browning or spots that resemble other problems.

Here’s how physical damage and pests can cause brown spots:

Physical Damage:
1. Wounding from Tools or Handling:
  - Problem: Accidental cuts, nicks, or bruises from pruning shears, garden stakes, or even rough handling can damage stems and leaves.
  - Impact: Any wound creates an entry point for pathogens, and the damaged tissue itself will die, forming a brown or black spot or lesion. On stems, these can become larger wounds.
  - Symptoms: Localized brown/black spots or areas where physical trauma has occurred.
  - Solution: Use sharp, clean tools for pruning. Handle plants gently. Ensure stakes or cages are installed early and securely without rubbing against stems.
2. Stem Splitting (from Overwatering or Rapid Growth):
  - Problem: Sometimes, if a tomato plant receives a sudden flush of water after a dry period, or experiences very rapid growth, its stems can swell faster than the outer skin can stretch, leading to splits in the stems.
  - Impact: These splits expose inner tissue, which then dries out and forms brown, calloused scars. While not necessarily harmful if they heal, they are a form of physical damage.
  - Symptoms: Vertical brown lines or cracks on stems.
  - Solution: Focus on consistent watering to prevent extreme fluctuations.
3. Hail Damage:
  - Problem: Hailstones can bruise and tear leaves, stems, and even developing fruit.
  - Impact: Impact points turn into small, irregular brown or black spots or tears.
  - Symptoms: Randomly distributed brown spots or tears, often on the upper side of leaves/fruit.
  - Solution: Cover plants with temporary protection (like buckets or old sheets) if hail is predicted.
Pests:
1. Tomato Hornworms / Other Caterpillars:
  - Problem: Large caterpillars like the tomato hornworm, or smaller ones like cabbage loopers, are voracious leaf-eaters.
  - Impact: They chew large, irregular holes in leaves, but they also leave behind dark green or black pellet-like droppings (frass) that can look like brown spots on leaves and fruit. While not direct damage to the tissue from a spot, the frass accumulates and can look like dark spots from a distance.
  - Symptoms: Large holes in leaves, defoliation, and visible dark droppings on leaves and fruit. You might also spot the large green caterpillars.
  - Solution: Hand-pick hornworms and drop them in soapy water. Use BT (Bacillus thuringiensis) spray for smaller caterpillars. Bonide Thuricide BT
2. Stink Bugs / Leaffooted Bugs:
  - Problem: These sap-sucking insects pierce fruit to feed.
  - Impact: Their feeding causes localized cell damage beneath the fruit skin, which manifests as small, irregular, whitish or yellowish areas that later turn brown and corky beneath the skin. On green fruit, the spots may be dark green and sunken.
  - Symptoms: Sunken, brown/corky spots on fruit, usually with a white, pithy area just below the skin. Pests themselves may be visible.
  - Solution: Hand-pick and destroy bugs. Use row covers early in the season to prevent them. Maintain garden cleanliness.
3. Spider Mites:
  - Problem: Tiny arachnids that thrive in hot, dry conditions.
  - Impact: They pierce plant cells and suck chlorophyll, causing a fine stippling (tiny yellow dots) on leaves. In severe infestations, the leaves will turn yellow, bronze, then brown and dry out, often accompanied by fine webbing.
  - Symptoms: Fine yellow stippling, leaves turning dull then bronze/brown, fine webbing, especially on leaf undersides.
  - Solution: Increase humidity. Spray plants thoroughly with strong water jets or insecticidal soap Safer Brand Insect Killing Soap or neem oil.

While less common than disease or environmental stress, physical damage and pests should always be considered when diagnosing brown spots on your tomato plants, as they require specific and prompt interventions.