Folchs clinical training at university included a period as an intern in the surgical clinic of Dr. Antoni Trias and as the sole physician in Almedret, a small Catalan village of 800 people. By contrast, the basic sciences consisted mainly of lectures with little opportunity for hands-on laboratory experience. Folch was fortunate to have the opportunity to study at the Institute of Physiology in Barcelona, which was founded by his uncle August Pi Sunyer and Jesus Maria Bellido and was dedicated to carrying out basic research using contemporary methods and ideas. He worked as an assistant to his cousin Cesar Pi Sunyer and by the time he received his M.D. degree, they had jointly published four papers on glycogen synthesis in three different languages (German, French, and Spanish). Folch also studied blood glucose and lactic acid metabolism under the direction of the man he considered his scientific mentor, Professor Rosend Carrasco Formiguera. He was the person who particularly encouraged the young Folch in his research. Folchs experiences at the Institute of Physiology intensified his interest in physiology and in clinical questions, particularly as they related to metabolic problems. Thanks to Carrasco's contacts, Francisco Duran Reynals, a biochemist at the Rockefeller Institute in New York, became interested in Folch and arranged for him to come to that institution as a volunteer.
In 1936, just before the Spanish Civil War broke out, he was accepted as a research fellow at the Rockefeller Institute in New York, and he took the post. At the insistence of his family (who had fought for the defeated Republican side—his brother Albert and sister Nuria had to exile into Mexico and his other brother Frederic spent a few months in prison after returning from exile in France), he decided to stay in the United States after the Civil War ended.