The greatest impact of the inquisition was the banishment of Islam from Spain. Muslims invading Spain and Portugal in the early 700s were, at first, tolerant of Christians and Jews. There was a cohabitation of Muslims, Christians, and Jews. It was when more fundamentalist Muslims came into control, they began to persecute Christians and Jews with brutal beheadings.
Then Isabel and Ferdinand came to the throne and reconquered the Muslim kingdom in Spain. For them, Spain was once again to become a Christian nation. They expected all Muslims and Jews to convert to Christianity or leave Spain forever. The Inquisition continued to hold strong suspicions that many people who converted falsely were practicing old beliefs in secret. These suspicions extended to Muslims as well, who were forced to convert in the early 1500s. The Inquisition would only put you to death if you refused to repent. It was a brutal regime, but so were the Muslims who persecuted Christians and Jews.
All regimes of the time were brutal by our standards. But Spain probably had the most civilized system of governance and justice in Europe.