Witch hunting was more of a Central-Northern European thing, so the scale of persecution in Spain (with the exception of Euskadi) was much lower than in, say, Germany. See this map. The Spanish inquisition main target was, after all, the conversos (muslims and jews, forced to convert to catholicism after the Reconquista), and to a lesser extent, Protestants. This was actually the reason that 'propelled' the Crown to establish it in the first place.
"The new tribunal of 1480 soon extended its authority over both Castile and Aragon. Its express purpose was to deal with the religious practices of the ‘conversos’ of Jewish origin. Virtually all the people it arrested and examined in the first thirty years of its existence were conversos" Golden Age Spain, Kamen
According to Kamen, the inquisition attitude towards witchcraft was fairly progressive for the time. I'd take this claim with a grain of salt though (Kamen do tend to 'overreact' a bit in rehabilitating the Inquisition. But consider that, after all, he's responding to an extreme view as well, that the inquisition was the summum of evil):
"The Spanish Inquisition played a part in prosecuting the phenomenon, but its role was surprisingly enlightened, for it insisted that ‘witchcraft’ was imaginary and therefore not a criminal offence. Whereas in most other countries witches were executed, the Spanish clergy (like those of Italy) refused to treat their offence as heresy, and clear directives from the Inquisition in 1526 and in 1610 made sure that the burning of witches was virtually unknown. However, the secular authorities in Spain continued to execute witches (by hanging), and the number of their victims may have been substantial" Golden Age Spain, Kamen
Given the reputation of the Spanish Inquisition, it will come as a surprise that persecution of witchcraft in the Iberian peninsula was far more 'restrained' than in the northern countries of the same period. This restraint is quantified in the smaller ratio of witches burned to witches prosecuted. There are several reasons for this.
Although we envision the persecution of witches as a uniform phenomenon, there was in reality a diversity of expressions of it in the late medieval and early modern periods: secular and religious prosecutions, rural mobs and aristocratic accusations, tribunals and royal assizes. Moreover, what underlay the accusations of witchcraft - not just maleficium, but sabbat, devil's pact, devil worship - was not consistent across Europe. Superficially speaking, this diversity is what actually makes it a challenge to the historian in understanding what lay at the root of the 'sudden' outbreak of persecution of witches.
The Spanish (and Portuguese and Roman) Inquisitions were centrally controlled within their respective territories, controlled by an office of inquisition. This is important in several respects for controlling the type and methods of persecution:
a) The Iberian inquisitions were focused on conversion and exclusion of Jews (and Muslims) in the first half century of operation with focus shifting to other heresies over decades and centuries, such heresies included protestantism and lutheranism; Catholic doctrine refuted the notion of broad based cabals of witches which was the feature and impetus of northern witch hunts;
b) the inquisition was driven by Catholic doctrine of salvation: the objective was conversion and saving of the heretic, of bringing the sheep back into the flock; death, expulsion were technically the last resort. This was policy, if not entirely reality, but by and large the main;
c) maleficium was always a debated issue within Catholic heresiology, and the notions of a devil's pact or collective conspiracy (sabbats) were generally discredited. Here we can look to the influence of 14th c Spanish inquisitor Nicholas Eymeric and his Directorium Inquisitorum and other inquisitor's manuals which focused on sorcery and not devil worship. Inquisition literature informed generations of office practice which created a consistency not found in northern persecutions;
d) because of (b) & (c) there was less room for exercising local enmities and politically-motivated accusations that featured so much in aristocratic and village persecutions in northern Europe, partly because of:
We should understand here that despite how the Catholic Church looms large in our imagination as a persecuting institution during this time, that persecution was tempered by innovations in judicial practice often ahead of secular institutions. This lead to a contradictory state (to us) where due process and legal technique resulted in less torture, and therefore less confessions of maleficium, or witchcraft - contradictory because we think of inquisition and torture as synonymous. Moreover, the reduced use of torture meant that there were less implicating of co-conspirators, that tinder of large scale burnings:
The restraint shown by both the Spanish and the Roman inquisitions in the use of torture had a predictable effect upon witch-hunting in the Mediterranean world. It did not completely prevent large witch-hunts from taking place, since local panics and dream epidemics were by themselves capable of supplying large numbers of suspects. But without the unrestricted use of torture the hunts that developed did not produce as many convictions or result in as many executions as the large hunts that occurred in Germany and Switzerland. Even more importantly, the reluctance to use torture prevented the development of extreme, diabolical witch beliefs. Without torture the potential for transforming simple acts of superstition into crimes of diabolical conspiracy was greatly limited, since only through confessions adduced under torture could diabolical beliefs gain the widespread legitimacy that was necessary to sustain further witch-hunting. Without torture it was certain that the learned as well as the popular view of witchcraft would remain essentially an individual moral transgression, not a large-scale attack upon Christian civilization. [Levack, The Witch-Hunt in Early Modern Europe, p240]
