The study comes on the back of numerous other studies supporting the practice, which is increasingly occupying shelf space in European supermarkets.
Food makers, after all, are waking up to the fact that ethical consumerism is a growing phenomenon and is a sector with disposable income.
Writing in the online edition of Proceedings of the National Academy of Sciences (PNAS), Stanford University graduate student Sasha B. Kramer and her colleagues found that fertilising apple trees with synthetic chemicals produced more adverse environmental effects than feeding them with organic manure or alfalfa.
"The intensification of agricultural production over the past 60 years and the subsequent increase in global nitrogen inputs have resulted in substantial nitrogen pollution and ecological damage," said Kramer.
"The primary source of nitrogen pollution comes from nitrogen-based agricultural fertilizers, whose use is forecasted to double or almost triple by 2050."
Nitrogen compounds from fertilizer can enter the atmosphere and contribute to global warming, adds Harold A. Mooney, the Paul S. Achilles Professor of Environmental Biology at Stanford and co-author of the study.
"This study shows that the use of organic versus chemical fertilizers can play a role in reducing these adverse effects," he said.
Other studies have suggested that modern farming practices have also led to nutrient-poor food. Dr David Thomas, a primary healthcare practitioner and independent researcher, recently made a comparison of government tables published in 1940, and again in 2002.
He found that the nutritional quality of vegetables has significantly fallen over the last few decades.
"Why is it that you have to eat four carrots to get the same amount of magnesium as you would have done in 1940?" he asked. Thomas argues that food manufacturers need to promote not just good looking, wonderful tasting and great smelling food, but also nutrient-rich food.
Such concerns have been absorbed by consumers, who have begun to demand better quality food. A recent study by the Co-operative bank suggests that UK spending alone on 'ethical' food, including organic, fair trade and free range, was up from £ 3.7bn to £ 4.1bn in the 2004-5 period.
Organic food is therefore now big business. The European market was worth € 20.7 billion in 2004, and has been growing by 26 per cent since 2001.
This most recently study will therefore likely reinforce consumer perceptions of organic food as something that is both better for the environment and the individual.
The PNAS study was conducted in an established apple orchard in central Washington, US, one of the country's premiere apple-growing regions.
Some trees used in the experiment had been raised with conventional synthetic fertilizers. Others were grown organically without pesticides, herbicides or artificial fertilization. A third group was raised by a method called integrated farming, which combines organic and conventional agricultural techniques.
"Conventional agriculture has made tremendous improvements in crop yield but at large costs to the environment," the authors write. "Organic farming cannot provide for all of our food needs, but it is certainly one important tool for use in our striving for sustainable agricultural systems."