Taubes gained prominence in the low-carb diet debate following the publication of his 2002 New York Times Magazine piece, "What if It's All Been a Big Fat Lie?". The article questioned the efficacy and health benefits of low-fat diets, was seen as defending the Atkins diet against the medical establishment and became extremely controversial (Taubes himself has stated "Even though I knew the article would be the most controversial article the Times Magazine ran all year, [the reaction] still shocked me"). The Center for Science in the Public Interest published a rebuttal to the Times article in their November, 2002,newsletter . According to Taubes, "[T]he CSPI is an advocacy group that has been pushing low-fat diets since the 1970s.".

In 2007, Taubes published his book Good Calories, Bad Calories: Challenging the Conventional Wisdom on Diet, Weight Control, and Disease, ISBN 978-1400040780 (published as The Diet Delusion in the UK, ISBN 978-0091891411). This aims to examine how a hypothesis became dogma and claims to show how the scientific method was circumvented so a contestable hypothesis could remain unchallenged. The book uses data and studies compiled from dietary research from as early as the 1800s.

Taubes' hypothesis is that the medical community and the federal government of the United States of America have relied upon misinterpreted scientific data on nutrition to build the prevailing paradigm about what constitutes healthful eating. Taubes makes the case that -- contrary to the conventional wisdom -- it is refined carbohydrates that are responsible for heart disease, diabetes, obesity, cancer and many other maladies of civilization. In the Epilogue to Good Calories, Bad Calories on page 454, Taubes notes ten "inescapable" conclusions, the first of which is:

Taubes includes information and studies which indicate that physical exercise increases appetite to a degree that makes it an inefficient tool in weight loss. He tracks the origins of commonly accepted dietary advice and aims to show that information that is filtered to the public often contradicts scientific evidence. On October 19, 2007, Taubes appeared on Larry King Live to discuss his book. Although Taubes has no formal training in nutrition or medicine, his book was praised as "raising interesting and valuable points" by Dr. Andrew Weil, a believer of alternative medicine, while Dr. Mehmet Oz and trainer Jillian Michaels who appeared on the same program disagreed with Taubes on many questions.

The reviews for Good Calories, Bad Calories have been variable. Dr.Bray notes in his review that "...has much useful information and is well worth reading." but "Obese people clearly eat more than do lean ones."Taubes in his letter to the editor of the same journal in response clarifies some of the comments made by Bray. Taubes notes, "The hypothesis favored by Bray and a half century of authorities on human obesity is that fat accumulation is fundamentally caused by positive energy balance..." Taubes responds, "The alternative hypothesis begins with the fundamental observation that obesity is a disorder of excess fat accumulation and then asks the obvious question, what regulates fat accumulation. This was elucidated by 1965 and has never been controversial. 'Insulin is the principle regulator of fat metabolism'..."

Taubes has won the Science in Society Award of the National Association of Science Writers three times and was awarded an MIT Knight Science Journalism Fellowship for 1996-97.