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There are some web-sites advocating that eating fruits separately to other foods is healthier.

When fruits are eaten alone, your stomach can more easily process all of the nutrients, fibre and the simple sugars contained in the fruit. This is the optimal 'proper way' to benefit from the fruit you eat.

Advocates of food combining also focus upon not including fruit as part of a meal. For example, a common recommendation is to wait at least an hour after consumption of any non-fruit foods before eating a piece of fruit.

They suggest dubious mechanisms - for example, from Mind Body Green:

If you eat fruit close to a meal, especially right after a larger meal and combine with other foods, it's held in the stomach too long along with other foods and will rot and ferment in the gut.

Whatever the mechanism, they claim benefits, such as from WH Foods:

many people do report better overall digestion when they follow this procedure and a large number of healthcare practitioners advocate fruit consumption separate from meals.

Snopes has an article on the subject.. It is is not very helpful, as it only quotes a few dieticians who disagree with the practice (none of whom cite any studies), which is no better than the sites that support it.

What do the studies say? Are there health benefits to eating fruits as a separate meal, rather than consuming the same amount with other foods?

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    I think you need to make your question more clear. Fruit combining can mean simply eating fruit at the same time as other fruits, or it can mean following a very prescribed method of choosing those combinations. It doesn't necessarily have anything to do with an empty stomach. What type of "effectiveness" would you like to know if studies have been done for?
    – user5582
    May 14, 2013 at 18:38
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    @jwenting: The claim is that eating fruit separately from your other foods (on an empty stomach, and/or much later or earlier in the day) is healthier than eating fruit with your other foods. I thought that was pretty clear from the question and the links. Of course, "healthier" is a loose term, but that same complaint could be made for the dozens of other similar questions asking if one thing is "healthier" than another. Considering that this is a pretty wide-spread claim in dieting and weight-loss books, I think it's certainly worth looking into.
    – BlueRaja - Danny Pflughoeft
    May 15, 2013 at 9:03
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    @BlueRaja-DannyPflughoeft Is your question about combining particular fruits together? Or is your question about eating them on an empty stomach. From my reading, I'm convinced these are two separate techniques.
    – user5582
    May 16, 2013 at 20:40
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    @BlueRaja-DannyPflughoeft This site that you reference doesn't say that eating fruits on an empty stomach is better. It just lists particular combinations of fruits that go well together, with the exception of melons, which they claim don't combine well with other fruits.
    – user5582
    Jun 16, 2013 at 17:58
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    Please provide a reference for people using "fruit combining" to mean eating on an empty stomach.
    – user5582
    Jun 17, 2013 at 5:55

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Is eating fruits separately healthier?

This answer isn't by far exhausting, but from what I've been able to find…

Probably not.

Arguments

Let's try to break down the individual claims and compare them with actual studies. Because it is hard to find studies specifically on fruits, I used studies that focused on dietary fiber, sugar and/or vitamins – things fruits are rich in. [1]

Does mixing fruits with other food slow down gastric emptying?

If you eat fruit close to a meal […] it's held in the stomach too long

I couldn't find any comparison of digest times of ‘fruit only’ vs. ‘fruit with other meal’. However, I found a study (Yu K., 2014) which compares digestion of meals with added dietary fiber to those without added fiber. Fiber was served as a drink with 7.5 g of dietary soluble fiber in it, which is slightly more than the amount of fiber found in 1½ medium apple (USDA). The study found an increase in the time it takes before the stomach to empties half its contents from 72 minutes to 86 minutes.

So while I can't verify the claim that “fruit alone is digested faster than fruit and a meal“ (which is probably also true since larger meals generally take longer time to digest), it has been demonstrated that “meal alone is digested faster than with fruit”.

Is slower gastric emptying a bad thing?

According to Nutrition by Erin, (I'm going to paraphrase it a little) the gastric emptying rate varies between people and depends on many factors. It can be too rapid (symptoms include weakness, diarrhea, and lightheadedness after a meal) or too slow (nausea, vomiting, abdominal pain, and fullness). If one's emptying rate is too slow, they should logically avoid things that slow it down even further, if one's rate is too fast, they can change their diet to help slow it down – eg. they can eat high-fiber foods. Otherwise, some variation in emptying rate is natural.

If you eat fruit close to a meal [it] will rot and ferment in the gut.

A meta-study by R. H. Hunt, 2015 states: “the stomach, together with the oesophagus and duodenum, is the least colonised region of the GI tract”, effectively only H. pylori can live in the acidic environment.

While there may[1], or may not[2] be a link between slower gastric emptying and H. pylori infection, it is reasoned that the infection causes slower gastric emptying, not the other way round.

In summary, it seems improbable that prolonged digestion in the stomach of a healthy individual, where no bacterial rotting and fermentation can occur, would cause rotting or fermentation in the intestine.

Does empty stomach process the fruits better?

When fruits are eaten alone, your stomach can more easily process all of the nutrients, fibre and the simple sugars contained in the fruit.

This is obviously hard to tell, because monitoring the nutrients of a food as it's being digested isn't a very straightforward task that you could do with ultrasound or X-ray. However there doesn't seem to be much reason for the claim to be true.

Vitamins: Water-soluble vitamins don't need any acids to disolve, fat-soluble vitamins do need special bile acids, but those are found in the intestine, not stomach. [1]

Fiber: Fruits have large amount of water-soluble fiber, higher than vegetable [2], so its digestion should be no problem. Not only that, soluble fiber “softens stool and helps slow the movement of the digested material through the digestive tract. This increases nutrient absorption and provides a feeling of fullness for a longer period of time, therefore reducing overall calorie intake. Soluble fiber also binds to bile acids in the intestines and promotes their excretion.”[3] Then there is insoluble fiber which can't be digested at all.

Sugars: Since the other food probably contains more complex carbohydrates, I don't see why there should be any problem with the digestion of the simple sugars found in the fruit. Furthermore, a recent study suggests that fructose, which had been thought to be processed in liver, is in fact mostly processed in the intestine. Only when the amount of fructose is too large, it is sent to the liver, which might be harmful. Therefore the autor suggests that sugar-rich food should be consumed after a meal, not on an empty stomach. However the study was done on mice and the real consequences aren't exactly well studied, so this might be a bit of a stretch.

Summary

While it seems to be true that mixing fruits with other meal prolongs the time that the food spends in one's stomach, there doesn't seem to be anything bad about it.

Further reading

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