Others, following a strain of Bosch-interpretation datable already to the 16th century, continued to think his work was created merely to titillate and amuse, much like the "grotteschi" of the Italian Renaissance. While the art of the older masters was based in the physical world of everyday experience, Bosch confronts his viewer with, in the words of the art Historian Walter Gibson, "a world of dreams [and] nightmares in which forms seem to flicker and change before our eyes". In one of the first known accounts of Bosch's paintings, in 1560 the Spaniard Felipe de Guevara wrote that Bosch was regarded merely as "the Inventor of monsters and chimeras". In the early seventeenth century, the artist-biographer Karel van Mander described Bosch's work as comprising "wondrous and strange fantasies"; however, he concluded that the paintings are "often less pleasant than gruesome to look at".

Over the years, scholars have attributed to him fewer and fewer of the works once thought to be his. This is partly a result of technological advances such as infrared reflectography, which enable researchers to examine a painting's underdrawing. Art historians of the early and mid-20th century, such as Tolnay and Baldass, identified between 30 and 50 paintings that they believed to be by Bosch's hand, while a later monograph by Gerd Unverfehrt (1980) attributed only 25 paintings and 14 drawings to him. In early 2016, The Temptation of St. Anthony, a small panel in the Nelson-Atkins Museum of Art in Kansas City, Missouri, long attributed to the workshop of Hieronymus Bosch, was credited to the Painter himself after intensive forensic study by the Bosch Research and Conservation Project. The BRCP has also questioned whether two well-known paintings traditionally accepted to be by Bosch, The Seven Deadly Sins in the Prado and Christ Carrying the Cross in the Museum of Fine Arts, Ghent, should instead be credited to the artist's workshop rather than to the painter's own hand.

A 2012 study on Bosch's paintings alleges that they actually conceal a strong nationalist consciousness, censuring the foreign imperial government of the Burgundian Netherlands, especially Maximilian Habsburg. By systematically superimposing images and concepts, the study asserts that Bosch also made his expiatory self-punishment, for he was accepting well-paid commissions from the Habsburgs and their deputies, and therefore betraying the memory of Charles the Bold.

Bosch did not date his paintings, but—unusual for the time—he seems to have signed several of them, although some signatures purporting to be his are certainly not. About 25 paintings remain today that can be attributed to him. In the late sixteenth century, Philip II of Spain confiscated and acquired many of Bosch's paintings, including some probably commissioned and collected by Spaniards active in Bosch's hometown; as a result, the Prado Museum in Madrid now owns The Adoration of the Magi, The Garden of Earthly Delights, the tabletop painting of The Seven Deadly Sins and the Four Last Things and The Haywain Triptych.

Bosch's paintings with their rough surfaces, so called impasto painting, differed from the tradition of the great Netherlandish Painters of the end of the 15th, and beginning of the 16th centuries, who wished to hide the work done and so suggest their paintings as more nearly Divine creations.

The exact number of Bosch's surviving works has been a subject of considerable debate. His signature can be seen on only seven of his surviving paintings, and there is uncertainty whether all the paintings once ascribed to him were actually from his hand. It is known that from the early 16th century onwards numerous copies and variations of his paintings began to circulate. In addition, his style was highly influential, and was widely imitated by his numerous followers.