Why do my apples have brown spots under the skin?

Calcium moves in the plant with water and goes preferentially to leaves rather than fruit. Anything that makes the tree's water supply erratic, or makes individual fruits very large, or makes the leaves grow vigorously, results in fruit that never got enough calcium — and that shows as bitter pit, often only after the apples have been in store for a few weeks. It is a physiological disorder, which is why spraying the soil with lime achieves nothing.

Step by step

1. Confirm the symptoms.Sunken dark green or brown spots up to a few millimetres across, mainly at the eye end of the fruit. Cut into one: dry, brown, corky flecks scattered in the flesh under the skin, tasting bitter. No mould, no tunnel, no wound.
2. Rule out the look-alikes.Scab is a surface crust that cracks. Codling damage has a tunnel and frass. Rot is soft, wet and spreading. Bitter pit is dry and corky, and the skin is intact.
3. Look at the fruit size and the crop load.Bitter pit is worst on large fruit from a light crop, which is why over-thinning causes it. If you thinned very hard and got enormous apples, that is likely the cause.
4. Fix the watering.Consistent moisture through July, August and September is the single most effective measure. Deep watering weekly in dry spells, and a mulch in spring so the soil does not swing between wet and bone dry.
5. Cut the nitrogen.Vigorous leafy growth competes with the fruit for calcium and makes bitter pit worse. Stop general fertiliser and lawn feed near the tree, and use sulphate of potash in late winter.
6. Prune less hard.Hard winter pruning drives vigorous growth for the same reason. On a tree with bitter pit, prune conservatively for a couple of seasons.
7. Do not over-thin.Thin to the normal spacing rather than beyond it. A moderate crop of normal-sized fruit gets more calcium per apple than a tiny crop of giants.
8. Consider calcium sprays only if the cultural measures fail.Foliar calcium applied to the fruit through summer is what commercial growers use, because it puts calcium where it is needed rather than in the soil. In a garden it is a last resort after watering and feeding are fixed, and any product must be approved for edible crops.
9. Store affected fruit separately and use it early.Bitter pit often develops or worsens in store. Fruit showing it will not keep and should be used first.

Tips

• Bramley, Newton Wonder, Crispin, Egremont Russet and Warner's King are all prone. If you have one of those on light soil, expect to have to manage watering.
• Light sandy soils and containers, which dry out and rewet repeatedly, produce the worst bitter pit. The mulch matters more there than anywhere.
• Fruit that looks clean at picking can develop pit in store, so a batch that goes spotty after a month in the shed was already affected at picking.
• Adding lime to the soil is almost never the answer, and on an already neutral or alkaline soil it will cause other problems.

Common mistakes

• Treating it as a disease and reaching for a fungicide — It is a physiological disorder caused by calcium not reaching the fruit. No fungicide affects it in any way.
• Liming the soil to add calcium — Most UK soils have plenty of calcium. The problem is transport into the fruit, not supply in the ground, and liming can lock up other nutrients.
• Thinning extremely hard to get show-sized apples — Very large fruit is the most affected. A moderate crop of normal fruit has far less bitter pit.

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