There is a difference in nutritional quality between the two.
A study published in the Journal of Applied Nutrition lists many nutrients that appear to be altered based on how they are farmed. The study looked at organic apples, pear, potatoes, wheat, and sweet corn and compared the levels of certain nutrients in relation to the commercially available counterparts produced via modern farming practices. The study lists the macronutrient chromium as being found at levels 78% higher in organic foods. The study also showed that Calcium is found at a level 63% higher in organic foods and Magnesium is found at a level 138% higher in organic foods. Other studies have shown that the use of pesticides can also alter the levels of certain vitamins including B vitamins, vitamin C, and beta-carotene in fruits and vegetables.
In 2003 a study was published in the Journal of Agricultural and Food Chemistry which found that organic corn had 52% more vitamin C than the commercially available counterpart which was grown utilizing modern farming practices. This study also found that polyphenol levels were significantly higher in the organic corn.
Washington State University did the right thing with strawberries. John Reganold and his colleagues took the same strain of berry and planted it in two plots of earth right next to each other. One patch was conventionally grown (with chemicals) and the other was raised organically.
Same soil, same weather, same strain of berry. The result? The organic strawberries had higher nutritional content.
In the recent infamous Stanford study that is raising a ruckus, the conclusion was: conventional and organic food are nutritionally equal. But no planting of food was done. No study was done at all, in fact. It was a review of prior published studies, and there is no indication that those prior studies handled crops the correct way, as the Washington State strawberry researchers did.
John Reganold, professor of soil science at Washington State University Regents and author of the new study, and his colleagues conducted the most comprehensive analysis of its kind on commercial produce soil and the strawberries that grow in it. (Conventional strawberries, as many now know, are one of the most pesticide-laden fruits available for sale.)
Reganold and his team analyzed 31 different chemical and biological soil properties--including soil DNA--and performed tests on the quality, nutritional value and taste of 26 different strawberries from both conventional and organic fields. And what they found is truly astounding.
Organic strawberries contain far more antioxidants, vitamin C and beneficial polyphenolic compounds than conventional strawberries, and they have a longer shelf life. Organic strawberries also contain more dry matter per volume--meaning more actual strawberry--than conventional ones do.
Plus all this doesn't take into account the pesticides and herbicides you ingest with conventional fruit.