What causes my zucchini to rot when only 3" or 4" long?
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There are two reasons that this happens:
Reason 1. The fruit develops a disease that is similar to tomato blossom end rot which happens when the water given to the plants is uneven which creates a calcium deficiency. This can be prevented by mulching to keep the soil moisture even, and by watering regularly to give the plants adequate water.
Reason 2. The second reason is that the flowers themselves develop a fungus and rot back into the fruit. This happens especially in areas or gardens that have high humidity, or where gardens are watered from above and plants are kept wet for long periods of time.
The Solution:
In either case mentioned above, the answer to the problem is super easy:
Simply remove the flowers once the young fruit has begun to swell and grow.
Plus - after you remove the flower, if you see any decay starting, take you fingernail and gently scrape the end of the fruit to remove any decaying material.
A small scar will form where you did this, but the rot will stop and your squash will develop into mature fruit with no further problems.
https://pender.ces.ncsu.edu/2013/05/why-are-my-squash-rotting/
If it is blossom end rot, there is one thing I found helpful with my potted tomato plant last summer. Potted plants go through the nutrition in the soil quickly because of having to water the plants more and not having the availability of nutrition in the soil like they do in the garden. When I saw my tomatoes were developing blossom end rot in the one I had potted, I went to one of my local greenhouses and purchased a calcium supplement you sprayed on the leaves. This doesn't cure what is already affected, but did stop it in any further tomatoes on the plant as they ripened. Reapply as the directions instruct you to keep the tomatoes healthy.
Check for bugs under the leaves and fruit