The Jews were expelled from Spain by royal edict in 1492 (the Alhambra Decree), being ordered to convert or leave, or be executed. Muslims were also expelled in other edicts. Therefore the population of Spain was, in theory, entirely Christian during the majority of the Inquisition. Your professor may know something I don't, but after 1492 it was punishable by death to be a non-converted Jew living in Spain.

The Inquisition focused on Christians who were suspected of still practicing their former faith, as well as anyone suspected of thinking Protestant thoughts. Spain wasn't just supposed to be Christian, it was supposed to be Catholic, and with total loyal to the monarchy. Other groups persecuted were those accused of witchcraft, blasphemy, Freemasonry, etc. So yes, the main target of the Inquisition were the conversos rather than openly Jewish communities because there were no openly Jewish communities in Spain after July 31, 1492. One could consider them free from interrogation, in that being found of practicing Judaism was grounds for immediate execution without a trial.

This is partially correct. The Spanish Inquisition only had powers to investigate deviations from Christian orthodoxy, therefore it only had powers over Christians, including recent converts (conversos and moriscos). Jews and Muslims can be brought to interrogation if they are suspected of influencing Christians to relapse into Judaism or Islam.

To give a better context, Isabella (and Ferdinand) intended for her dominions to be uniformly Catholic. This is part of a larger plan in increasing royal power over all aspects of life.

That the Inquisition should be under crown control was immediately seen as an advantage, in particular by Ferdinand. The two agreed and insisted to the Pope that the new institution be firmly under control of the Spanish crown.

Isabella and Ferdinand took the older existing inquisition of Sicily, then under the Crown of Aragon, and gave it a merced such that it could keep 1/3 of the property it confiscates from proven heretics (which in this context I use to mean converts who are not genuine, or non-Christians proselytizing their religion). This turned the inquisition into one that provides merced similar to that given to nobles contributing in the Reconquesta. This new system was quickly propagated to the rest of Aragon. Finally, it was introduced to Castille.

It is important to view the political context of the time. The Catholic monarchs had designs to change the political system of Spain, against the interest of the aristocratic class. They had founded the santa hermandad, the holy brotherhood, with them at its head, as a "national" police force that is supported by additional local taxes. This gave them significant power against local nobility, as they had the power to investigate, judge, and execute. There were many strong arguments in support of such an institution, as crime was unacceptably high in that period following Henry IV Castille's incompetent rule. When the Spanish inquisition was founded, evidence suggests they had similar ideas, although in most literature Ferdinand was seen as the true architect.

To quote Ferdinand, "The hermandad would soon be joined with an Inquisition and, together, employed as an instrument of terror and obedience."

To clarify, my professor in Spain said that people who were openly Jewish or Muslim were not targeted because while not necessarily socially advantageous, it was not illegal to be Jewish or Muslim. It was however illegal to lie about being Christian.

I ask because the common view of the Inquisition is that they tried to convert thousands of non-believers to Christianity and I had thought that was a myth.