Following the precedent of contemporary manuscripts of the Bible, Gutenberg and his associates devised a page layout that would help readers to find their way through the text and to identify its various constituent parts. To guide as well as please the eye, they allocated space for rubrication and ornamental initials designed to demarcate different portions of the Bible. They did not intend to produce a luxury book with a lavish amount of illustration, but they planned it to be large enough that it could be easily read out loud in a monastic refectory. A reader standing at a lectern could rely on various graphic devices to point to the proper place: headlines identifying the book of the Bible at the top of the page, rubrics signaling the beginning and the end of different sections, and ornamental initials of various sizes indicating the transitions between prologues, books, and chapters. A complete Gutenberg Bible contains 3,945 rubrics as well as 72 six-line initials, 3 five-line initials, 61 four-line initials, 11 three-line initials, 1,292 two-line initials, and 2,509 one-line initials

The three copies at the Morgan have varying amounts and levels of ornamentation. Several artists were responsible for the elaborate decoration of the vellum copy. A German illuminator thought to have been working in or near Mainz executed the exceptionally large eight-line initial P (an exception because the printers usually allocated six lines for this type of initial, but here they wished to accentuate the shape of the letter). This and other initials by this artist display stylistic features evident in three other copies and almost identical to specimens illustrated in a contemporary manual of manuscript illumination known as the "Göttingen Model Book." The vellum copy then passed into the hands of an illuminator in or near Bruges who continued on in quite a different style and supplemented the German work with additional ornament in the borders and between the columns. At some later date a collector cut out three leaves and many of the border decorations, which were replaced in facsimile. The facsimiles are quite possibly the handiwork of the Paris artist and lithographer Adam Pilinski (1810–1887), who is known to have restored two Gutenberg Bibles and to have worked for a former owner of that copy. His sleight of hand was legendary in his day, and, if he was the one who supplied the missing leaves and border decorations, he is responsible for having fooled more than one unwary scholar. The ornamentation in the two-volume paper copy consists mainly of penwork initials with rubrication in red and blue. If less ostentatious, it is better preserved than most surviving copies.

The Old Testament copy contains illumination attributed to the Fust Master, an artist who made his living by decorating books published by Fust, not just the Gutenberg Bible but also a number of Fust and Schöffer imprints. Indeed, an art historian was able to make that attribution on the basis of several books at the Morgan, including a 1465 edition of Cicero's De officiis (PML 975) and the 48-line Bible of 1462 (PML 19208–9). At first, four books were attributed to him, but the list has now grown to more than a dozen. It is thought that he could have been making an allusion to his employer by using a crossed knotted stick motif, which also occurs in Fust and Schöffer's printer's device. This motif could be a visual pun on the Latin word for a knotted stick or club, fustis. Here it is on the first leaf of Proverbs, which would ordinarily have been the first leaf of the second volume.

The Fust Master's highly original and easily recognizable style represents a transition between technologies—and not an easy one because he had to keep up with the output of the press. He devised painting techniques suitable for mass production, an entirely new approach mandated by the invention of printing. He employed the same palette and standardized motifs in several copies of the same book, identical designs repeated so frequently as to raise questions whether he had been using stencils. These striking similarities can be seen by comparing the Old Testament copy with the copy at the Biblioteca Pública Provincial, Burgos, Spain, which was also illuminated by the Fust Master. (A color facsimile of the Burgos copy was published in 1995–1997.) This decorated initial E is a typical example of a design that appears in the same place in both copies.

Note: The illuminated leaf at the beginning of Maccabees I (II, 162) is a facsimile, and a missing portion of leaf II,182 has been replaced with text in facsimile.