Soon after Dean Peacock came to Ely he commenced the restoration and decoration of the fabric which have gone on continuously to the present time, and are not yet complete. Besides many munificent gifts, of which the cost is not known, upwards of £70,000 has been expended upon the works at the cathedral since 1843. The first great work included in this sum was the entire re-leading of the roof. In 1842 there had been a fire discovered in the roof near the west tower, but no great damage was done. Most likely it was the prospect of having to spend large sums upon the cathedral itself that induced the dean and chapter to sanction the demolition of the sextry-barn, "on the ground that the repairs it required were too expensive." This barn was situated to the north of the lady-chapel. It was an object of the greatest architectural interest, and its destruction is much to be lamented. It was of Early English date, and is said to have been a "noble and almost unrivalled" building. It seems to have been of the same character as the abbey tithe-barn at Peterborough, which was perfect a very few years ago, and of which the whole of the wooden posts and beams are still to be seen in situ. The Peterborough barn was also of thirteenth century date; it had aisles and nave all formed by the oak beams and supports. The Ely barn was much smaller.

In July, 1845, the restoration had been well begun, and was being carried on with energy. The works in Bishop Alcock's chapel had been commenced. The south end of the west transept, hitherto used as a kind of storehouse or lumber-room, was repaired and thrown open to the church. A poor deal roof was added as a temporary protection. The choir roof was scraped and cleaned. In the lady-chapel the colour-wash that had obscured the remains of the beautiful carvings was removed. The west tower was ceiled. Up to this time there appears to have been no properly qualified architect in charge of the work. In 1847 Mr. Scott (afterwards Sir G. G. Scott) was appointed architect to the cathedral. He soon made an extensive examination of the whole building, and issued a report upon the state of the fabric and the amount of restoration needful.

Dean Peacock, who so thoroughly identified himself with the restoration, died in 1858. His successor, Dean Goodwin, entered with enthusiasm upon the work, and was instrumental in raising large sums of money for the carrying out of the architect's designs. After he had been dean seven years he published a paper upon the progress that had been made, which commences with these words: "The time seems to be now come, when the completion of the great work of restoration, commenced under Dean Peacock, and guided for many years by his care and judgment, may be looked upon as within reach."[29] In this paper he enumerated these works as already accomplished:

Of the painting the north transept roof the expense was borne by the tradesmen employed upon the cathedral. The restoration of Bishop Alcock's chapel was undertaken, out of respect to the memory of their founder, by Jesus College, Cambridge. The painting of the nave ceiling was the work of Mr. le Strange and Mr. Gambier Parry, the former of whom also painted the ceiling of the west tower. Exclusive of special donations for specific works included in the above list, the dean reckoned that up to the time of his report £27,185 had been spent, of which the dean and chapter had contributed no less than £15,200. Several individual members of the chapter had, besides money gifts, presented windows or other decorations, or had been responsible for various structural repairs. At a rough estimate the total sum expended had amounted to £40,000. The works still to be executed were these:

There would also be much to be done in the matter of properly warming and lighting the cathedral; but those expenses were more strictly within the ordinary obligations of the dean and chapter.

The only one of the above works that calls for special notice is the restoration of the octagon and lantern. In a statement circulated by the dean and chapter in 1853 it was declared that "of all works which remain to be undertaken, the most considerable and the most important is the restoration of the lantern, including the decoration of the vault, the substitution of windows of an appropriate character for those which now disfigure it so seriously, and the addition of the outer corona of turrets and pinnacles as originally designed by Alan de Walsingham." But nothing was done towards this during Dean Peacock's lifetime. In the summer before his death he had described more particularly the disfigurements and the mutilations which the lantern had undergone; and he further pointed out the unsafe condition of the exterior. The upper windows of the octagon were of the "meanest description of carpenter's Gothic"; they had been reduced from four to three lights each; they had been shortened more than three feet (probably by Essex in the eighteenth century); the upper timbers were in a ruinous state, and incapable of being used again. The original design provided for eight lofty turrets at the angles of the greater octagon and four pinnacles in the middle of its longer sides. At the first meeting of the chapter after Dean Peacock's death it was resolved that no memorial of him would be so appropriate as the restoration of the lantern, and Mr. Scott was instructed to prepare designs at once. A tentative sketch of his design was published in October, 1859; and the opinion of experts was invited. Mr. Scott's report, dated June 10, 1859, gave the result of his careful examination. He concluded that the wooden lantern was originally "to a certain extent an imitation of the general form of the stone octagon below it. Each had large windows of four lights below, with circular panels in the spandrils; each had a distinct story over these windows, lighted by smaller windows consisting of several detached lights, and each had considerable turrets, probably surmounted by pinnacles at the angles, and, in all probability, open parapets between them."[30] He embodied the results of the evidence he had got together in the design he submitted. Further examination, in the following year, satisfied the architect that no spire had ever been erected on the lantern, and that even if Walsingham had ever intended to have one, he had yet finished his work without any preparation for such an addition. A design for such a spire was, however, prepared and submitted to the dean and chapter, but it was never adopted.

As was to be expected, many opinions were expressed upon the design. Some wanted the whole to be surmounted by a pyramidal capping. It was objected that the design was a stone construction for what must of necessity be erected of wood. It was pointed out that Walsingham used his upper story as a bell-chamber, and argued that a true restoration should aim at reproducing this feature. In the end Scott's design was carried out exactly as proposed, except that the eight small square turrets of the wooden lantern have no pinnacles.