Debate continues as to whether the accusation of religious heresy had merit by the standards of the time. Under torture, some Templars admitted to homosexual acts, and to the worship of heads and a mystery known as Baphomet. Their leaders later denied these admissions, and for that were executed. Some scholars discount these as forced admissions, typical during the Inquisition. Others argue that these accusations were in reality due to a misunderstanding of arcane rituals held behind closed doors which had their origins in the Crusaders' bitter struggle against the Saracens. These included denying Christ and spitting on the Cross three times, as well as kissing other men's behinds.

According to some scholars, and recently recovered Vatican documents, these acts were intended to simulate the kind of humiliation and torture that a Crusader might be subjected to if captured by the Saracens. According to this line of reasoning, they were taught how to commit apostasy with the mind only and not with the heart. As for the accusations of head-worship and Templars trying to syncretize Christianity with Islam, some scholars argue that the former referred to rituals involving the alleged relics of Saint Euphemia, one of Saint Ursula's eleven maidens, Hughes de Payens, and John the Baptist rather than pagan idols. The latter they ascribe to the chaplains creating the term Baphomet through the Atbash cipher to mystify the term Sophia (Greek for "wisdom"), which was equated with the Logos (Greek for "Word"). This is a controversial interpretation, and is partly based on conjecture.

Conspiracy theories related to the suppression of the Knights Templar often go far beyond the suggested motive of seizing property and consolidating geopolitical power. It is the Catholic Church's position that the persecution was unjust, that there was nothing wrong with the Templars, and that the Pope at the time was manipulated into suppressing them. In 2001, Dr. Barbara Frale found the Chinon Parchment in the Secret Vatican Archives, a document that shows that Pope Clement V secretly pardoned the Knights Templar in 1314.

As he burned at the stake, Jacques de Molay, Grand Master of the Knights Templar, cursed King Philip and Pope Clement to meet eternal justice within the year. Pope Clement died only one month later and Philip IV seven months after that. Commentators were extremely pleased with such a development and often featured this story in their chronicles. The rapid succession of the last direct Capetian kings of France between 1314 and 1328, the three sons of Philip IV the Fair, led many to believe that the dynasty had been cursed – thus the name of "cursed Kings" (rois maudits).

The Knights Templar later became surrounded by legends concerning secrets and mysteries handed down to the select from ancient times. Perhaps most well known are the those concerning the Holy Grail, the Ark of the Covenant, and secrets of building. Some sources say the Holy Grail, or Sangreal, was found by the order and taken to Scotland during the scourging of the order in 1307, and that it remains buried beneath Rosslyn Chapel. Some say that the order also found the Ark of the Covenant, the chest which contained sacred objects of ancient Israel, including Aaron's rod and the tablets of stone inscribed by Moses with the Ten Commandments.

These myths are connected with the long occupation by the order of the Temple Mount in Jerusalem. Some sources record that they discovered secrets of the Master Masons who had built the original and second temples secreted there, along with knowledge that the Ark had been moved to Ethiopia before the destruction of the first temple. Allusion to this is made in engravings on the Cathedral at Chartres (considered along with the Cathedrals at Amiens and Reims to be one of the best examples of gothic architecture), great influence over the building of which was had by St. Bernard of Clairvaux, who was also influential in the formation of the order. Further links to both the search by the order for the Ark and to its discovery of ancient secrets of building are suggested by the existence of the monolithic Church of St George in Lalibela in Ethiopia, which stands to this day and whose construction is incorrectly attributed to the Knights Templar. There is also an underground church dated to the same period in Aubeterre in France.

Templars are also supposedly listed among the crew of Henry Sinclair's (Earl of the Orkneys) legendary voyage from Scotland to North America in 1398. There is growing speculation surrounding relics that would indicate the possibility that the Knights Templar possessed the charts of pre-Columbian voyages to America. Christopher Columbus' navigators were members of the extant Portuguese Templar Order, and the Templar cross was featured prominently on the sails of his ships in 1492.

Fringe researchers and aficionados of esotericism have claimed that the order stored secret knowledge, linking them to the Rosicrucians, the Priory of Sion, the Rex Deus, the Cathars, the Hermetics, the Gnostics, the Essenes, and, ultimately, lost relics or teachings of Jesus such as the Shroud of Turin or a "Judas Testament."