Estes was born January 10, 1925 to John and Lillian Estes on a farm near Clyde, Texas. He was one of six children. He did not attend college, but served in the U.S. Merchant Marine during World War II.  In the late 1950s, Estes was heavily involved in the Texas anhydrous ammonia business. He produced mortgages on nonexistent ammonia tanks by convincing local farmers to purchase them on credit, sight unseen, and leasing them from the farmers for the same amount as the mortgage payment, paying them a convenience fee as well. He used the fraudulent mortgage holdings to obtain loans from banks outside Texas who were unable to easily check on the tanks.  At the same time, United States Department of Agriculture began controlling the price of cotton, specifying quotas to farmers. The program included an acreage allotment that normally was not transferable from the land it was associated with, but which could be transferred if the original land was taken by eminent domain.  Estes worked out a method to purchase large numbers of cotton allotments, by dealing with farmers who had been dispossessed of land through eminent domain. He convinced the farmers to purchase land from him in Texas and transfer their allotments there, with a mortgage agreement delaying the first payment for a year. Then he would lease the land and allotments back from the farmer for $50 per acre. Once the first payment came due, the farmer would intentionally default and the land would revert to Estes; in effect, Estes had purchased the cotton allotments with the lease fees. However, because the original sale and mortgage were a pretext rather than a genuine sale, it was illegal to transfer the cotton allotments this way. Estes, however, a smooth talker revered by many of his fellow members of the Churches of Christ, asserted the allegations as politics.

Eventually, Estes’ schemes collapsed, and in 1963 he was tried and convicted on charges related to the fraudulent ammonia tank mortgages on both federal and state charges and was sentenced to 24 years in prison. His state conviction was later overturned by the United States Supreme Court in Estes v. Texas, 381 U.S. 532 (1965). His appeal hinged upon the alleged impossibility of a fair trial due to the presence of television cameras and broadcast journalists in the courtroom. He prevailed by a 5-4 vote. Estes was paroled in 1971. Eight years later, he was convicted of other fraud charges and served four more years.

Oscar Griffin, Jr., the journalist who uncovered the scandal, later received the 1963 Pulitzer Prize. His articles for a weekly newspaper in Pecos, Texas outlined how the businessman masterminded a Byzantine scheme to borrow money using nonexistent fertilizer storage tanks as collateral, leading to the FBI’s investigation. To improve his 1961 candidacy for Reeves County school board, Estes offered the local newspaper large advertising buys in exchange for not opposing him. The Pecos Independent responded with an editorial that said, “We will put our advertising columns up for sale, as will any other newspaper, but we WILL NOT sell our editorial support.” In response, Estes launched the rival Pecos Daily News on August 1, 1961. He spent about $600,000 and the Independent lost $400,000. It was nearly bankrupt when Griffin, its editor, ran (February 12, 1962) the first of four articles describing Estes’s fraud but without naming him. Estes was arrested ten days after the last article ran in March. After his arrest, the Daily News went into receivership; the Independent bought it and merged the two newspapers into the Pecos Enterprise. When Griffin died in 2011, Estes remarked, “It’s a good riddance that he left this world.”

In 1962, after information came to light that Estes had paid off four Agriculture officials for grain storage contracts, President John F. Kennedy ordered FBI agents be assigned to investigate Estes and the Justice Department also conducted an investigation which concluded that Orville L. Freeman, then Secretary of Agriculture, was “untainted”. Thereafter, Congress held hearings into this matter and other Estes activities including some that led to Vice President Johnson, who had been a business associate of Estes. Some historians say the vice president tried to help Estes with questionable dealings with the Agriculture Department after the storage tank fraud had been exposed. Others noted that Kennedy may have considered dropping Johnson from his ticket in 1964, partly because of the Johnson-Estes connection. Attorney General Robert Kennedy did have FBI director J. Edgar Hoover assign agents to investigate Estes in relation to the ties to Johnson. Hoover reported that they were unable to find any hard evidence as to the allegations against Johnson in his dealings with Estes.

Estes also alleged in the 1980s that he had inside knowledge that Johnson was involved in the assassination of Kennedy. In 1984, he provided a voluntary statement to a Grand Jury in Texas alleging that the homicide of a key investigator in the Department of Agriculture case was perpetrated by an aide to Johnson, Malcolm Wallace, upon orders from the then-Vice President. Henry Marshall had been the lead USDA inspector into the activities of Billy Sol Estes and he was killed at his ranch in Bryan, Texas on June 3, 1961. The death was ruled a suicide but over twenty years later a grand jury concluded the death was a homicide. When the Department of Justice asked for more information, Estes responded that he would provide information on eight other murders ordered by Johnson, including the assassination of Kennedy, in exchange for immunity from prosecution and a pardon. According to Estes, Johnson set up the assassination in order to become president. They refused.

Estes reiterated the claim in a book he co-wrote with a French writer in 2003. He said that he was not interested in writing the book – published only in France – but that he was offered “a few hundred thousand dollars” to contribute to it. According to the Associated Press, the allegation was “rejected by prominent historians, Johnson aides and family members.”