Ecclesiastical and monastic libraries, town libraries, school and university libraries are known as institutional libraries. They were the property of ecclesiastical or government institutions. The first university library in the northern Low Countries was founded in Leiden in 1586.

During the sixteenth century, town libraries were established in several towns (Hoorn 1535, Deventer 1590, Amsterdam 1578, Alkmaar 1594), based on the idea that libraries ought to be open to all interested members of the Republic of Letters. The term 'Bibliotheca Publica' does not refer to public accessibility, however, but indicates that the library belonged to an ecclesiastical or government body. Access was allowed only to educated, academically trained men.

Grammar schools usually had a small collection of books; where possible teachers turned to town libraries.

Around the year 1500, a few hundred monastic libraries existed in the Netherlands, most of which presumably held no more than a few dozen books. Most important were those of the Carthusian monasteries and of the houses of the Devotio Moderna. The library of the Heer Florenshuis in Deventer, probably the largest collection in the country, owned more than one thousand volumes of manuscripts as well as printed books.

During the Eighty Years' War, many libraries together with their books went up in flames or were otherwise destroyed. One of the few surviving collections is the library of the Carthusian monastery Nieuwlicht near Utrecht. Other collections were confiscated after the Reformation and transferred to town or university libraries.

Forced by limited budgets, librarians sought patrons to donate money or books to supplement the collections. The names of donors are often displayed in catalogues, with a list of the books they had presented. Usually, the gift was also noted in the books themselves.

Library visitors frequently had to put up with all sorts of inconveniences when they wished to consult the books: a long route by way of corridors and stairs to the upper floors of churches or convents, unheated rooms with little light and poor furniture, forcing one to remain standing. Reference works were often chained to the bookcases, making consultation of different volumes simultaneously a difficult task. Opening times were usually limited to a few hours a week.

In the period discussed here, catalogues or inventories existed as handwritten lists which could only be consulted on the spot. Apart from catalogues in book form, wall catalogues could be used or lists attached to each bookcase indicating the books placed on the shelves.