I've had the same problem and was able to get rid of the fruit flies using the following method.
First, sprinkle diatomaceous earth on the dirt in the plant pots. Diatomaceous earth is all natural and non-toxic, but it will kill the fruit flies.
Here's a link for killing bugs naturally with diatomaceous earth:
How to Get Rid of Spiders Naturally with Diatomaceous Earth
Next, make a mild soap and water solution, pour it in a spray bottle and spray the plants. Make sure the solution is mild because if it's too strong it will affect the plants.
Here's a link for the homemade insecticide soap recipe:
How to Make Homemade Insecticidal Soap for Plants Today Homeowner
The combination of the diatomaceous earth and insecticide soap will take care of your fruit fly problem. It will probably take about a week or so for all of the fruit flies to die, but if you're vigilant you'll take care of the problem.
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