Heresy trials usually resulted in convictions. The inquisitors would then hand the convicted heretics over to the secular authorities for punishment. Standard punishment for a first time offender was a long, solitary pilgrimage. When the heretic returned, they were forced to sew a yellow cross on their clothes, and wear this for life.

The accused were forced to stay in prison for the duration of their trial. It was not uncommon for their property to be confiscated, stolen or sold. Once the trial concluded, the accused was sent back to prison to await their sentencing. Defendants commonly waited years to find out the results of their trials. The inquisitors would store up cases and call another mass assembly of townspeople to announce several case results at once.

The inquisitors reserved burning at the stake for the most severe cases, usually those that were unrepentant or repeat offenders. Because murder is strictly against Catholic faith (ironically, this is overlooked in the Crusades), the inquisitors would have secular officials carry out the death penalties. However, this was considered a last resort, because their main goal of the inquisition was to save the heretical souls – not to commit murder.