The Moor population was subjected to conversion, voluntary or forced, under threat of expulsion. Between the Santa Hermandad and the Spanish Inquisition, this meant that that region became very Spanish, or to be more precise, Castilian. During the reign of Isabela, her confessor Cisneros even published a book of grammar to ensure orthodoxy.

There were Moorish and Morisco rebellions throughout, in addition to violence against them, but in the end orthodoxy prevailed. During the Spanish - Ottoman war, there were fears that Ottoman agents would invade and that the Moors and Moriscos would join them.

Catalonia was under the Crown of Aragon, one of the three crowns of Spain (the others being Castile&Leon, and Navarra). It had its own Cortes, laws, and strong identity. Due to many reasons, these crowns were never fully integrated into one Spanish system. If we are to speak of the time of Isabela and Ferdinand, their marriage united the crowns of Castile&Leon and Aragon. Afterwards, the western part of Navarre was conquered. During that reign, and successive Habsburg rule, Aragon was undergoing an economic depression. By contrast, Castile had a large population and very reliable tax base. As a result, the Cortes of Aragon was effectively governed from Castile. Navarre was left alone as it had the combination of a good (easy to control) system yet little tax income.

This is not to say there were no discontent in that era. Even Castile at first resisted Carlos I / Charles V as he was seen an outsider. Under Philip IV, the Count-Duke Olivares attempted to create a standing army based on contributions from all the crowns. Aragon was asked to contribute more troops and also to house tercios from Castile. This led to rebellion that nearly succeeded, except for quick intervention from Castilian troops. Soon after that rebellion broke, Portugal - who had been United under Philip II - rebelled and stretched the limits of the troops. As a result, Portugal regained its independence but Catalonia did not.

During the Spanish war of succession, the Navarre Cortes put its support behind the winning Bourbons. So their Cortes and Fueros were left mostly intact, while Aragon was merged into Castile. This led to suppression of Catalonian identity, which became worse during the Carlist wars and the Spanish Civil War, in addition to suppression of Navarese identity as both sides with the losing Republicans.