A federal grand jury in Chattanooga returned the four-count indictment against Barney Davis, 38, of Lewisburg, Christen Altman, 25, of Shelbyville, and Jeffery Bradford, 33, also of Lewisburg.
The offences alleged are breaches of the federal Horse Protection Act.
The indictment alleges the three conspired to violate the act by soring horses and falsifying entry forms and related paperwork.
United States Attorney Bill Killian said: "The alleged violations in this indictment undermine the equine industry and give unfair advantage to some over others, in addition to causing cruelty to the animals."
The indictment described soring as a cruel and inhumane practice.
It said Davis owned a business training and boarding spotted saddle horses, which he was responsible for preparing for horse shows.
It alleged the object of the conspiracy was to sore horses in order to win competitions without being detected by authorities, thus obtaining more customers who would pay Davis to board and train their horses.
The indictment alleged Davis and others known and unknown to the grand jury used various methods to sore horses before competition to improve their gait, with such soring methods to include placing bolts in horses' feet, taping blocks to horses' feet and other soring methods.
It was further alleged that Davis would try to mask the soring efforts by removing the exterior soring devices before inspection and giving horses shots to reduce the level of their reactions to inspections.
The indictment also alleges that, as part of the conspiracy, Davis would try to protect himself from being cited or ticketed for violations by using nominees to enter the show horses he was hired to train to deceive inspectors and cause them to ticket the nominee trainer instead of Davis.
Davis, Altman and Bradford are alleged to have falsified entry forms and other paperwork associated with various shows by deliberately and falsely claiming that Bradford and others were the trainers for particular horses that Davis has actually trained.
It is alleged that from about 2002 to October 2010 Davis directed individuals to sore horses in his care, including, but not limited to, the use of bolts in horses' feet and taping blocks to their feet.
Assistant US Attorney Steven Neff will prosecute the case.
Further allegations are outlined in the indictment, which can be read here.