At the end of the sixteenth century, as it had been before, philosophy was an integral part of the formal educational programme. In fact, at the very beginning of the studies in the college of arts, students had contact with logic, and the required texts were Porphyry’s Isagoge, and the Categories, De interpretatione, and Topics of Aristotle. However, as far as Jesuit colleges were concerned, the first text, i.e., Porphyry’s small book, lost its mandatory status for at least two and a half decades (perhaps more) from 1599 to 1623, that is, from the time that the Jesuit Ratio Studiorum recommended Fonseca’s Isagoge Philosophica until the last printed edition of this book by Fonseca. The reason was that Porphyry’s Isagoge was perceived as incomplete, incorrect, and unreliable. On the other hand, the Isagoge Philosophica of the 'Portuguese Aristotle' (as Pedro da Fonseca was also known) aimed to be faithful to Aristotle insofar as Aristotle’s doctrines coincided with the truth, and to draw its contents from the best authors of the Schools and from the vocabulary and the distinctions generally accepted by Fonseca’s contemporaries. Nevertheless, the success of Fonseca’s last printed work (at least 18 editions), was marred by controversy, since not even within the Jesuit order it was equally appreciated and accepted as a fitting introduction to philosophy. Leaving aside personal and national rivalries, we propose to examine the content of the Isagoge Philosophica, more precisely, its moderate realism, its psychological doctrines, and its ability to handle the main issues in and around Porphyry’s Isagoge in order to show that Fonseca’s work was opposed by some of his fellow Jesuits probably due to the latter’s incomprehension and limitations, rather than to lack of value or interest on the part of Fonseca’s Isagoge Philosophica. Our research also hopes to show that a true understanding of Jesuit philosophy and theology and of the philosophical and scientific developments of the early modern period gain new light once Fonseca’s systematic view is discovered and examined starting from his last published work, i.e., Fonseca's system in which dialectics, cognition, and metaphysics form a whole, can be established starting from a careful study of his Isagoge Philosophica.