In 1940 when Germans forces occupied the Channel Islands, the Temple building with the exception of the caretaker's living quarters, was closed, and the German authorities gave an undertaking that provided all Masonic activities ceased, nothing would be done to interfere with the premises or its contents. Relying on this assurance, the Provincial Grand Master, RW.Bro C.E.Malet de Carteret gave instructions that the premises were to remain locked, and that nothing need be removed. Unfortunately, this reliance was very much misplaced, and a squad of what can best be described as wreckers and looters, sent directly from Berlin, started the sack of the Temple on the 27th January 1941 which continued for two days. They were watched at a discreet distance by Bro G.S.Knocker, the Librarian and Curator of the Jersey Masonic Library and Museum. It is hard to try to imagine the distress that must have been felt by him, at seeing his hard work in building up the collections of books and other items so wantonly destroyed.

The Nazis left very little in the Temple, just the portraits by John St.Helier Lander and the Masters' boards which were fixed on the walls. The warrants that had hung in the ante-room were all removed. Of the furniture, regalia, Lodge books, etc, there was no sign. Much had been destroyed in a bonfire in the caretaker's garden adjoining the Temple. What was of value to the Nazis politically, had been shipped to Berlin. The pair of Cary's Globes dated 1806 (Terrestrial) and 1799 (Celestial) that had been situated either site of the Master's pedestal were never recovered. These globes would now be worth in excess of £30,000. The boiler was left in a dangerous state and could not be used. The chequered carpet had been removed to Linden Court, St.Saviour, the accommodation used by Col. Schumacher, the German Civil and Administrative Commander, who had taken it back to Germany with him in 1941.

During the Occupation the German authorities had forced the States of Jersey to pass an Act to enable the property, both real and personal, to be transferred out of the hands of the Masonic authorities to themselves, and this led to some problems in gaining early access to the Temple after the Liberation. The negotiations with the civil and military authorities were lengthy and complicated, but by the 18th July 1945, W.Bro Knocker was able to regain access. The condition of the building internally was terrible, as it had been used as a store for bottles of wine and the confiscated radio (or wireless) sets. Much work had to be done to restore it to some semblance of order.

The Management committee established a special bank account with the Midland Bank, Hill Street, entitled the "Restoration Fund." All Lodges were requested to collect from each of its members a sum equivalent to two years subscription and pay these into this Fund. Provincial Grand Lodge made a donation of £1,000 towards the rehabilitation and refurbishment of the building. However it needed much effort by the brethren of the Province to make the building habitable again. It is to their credit that the work was completed within a comparatively short time.

Many gifts were received towards refurbishing the Temple including three pedestals, three tracing boards, heavy maul, rough and smooth ashlars, tripod and stand, tool box, twelve sundry aprons, three collars. Many of these were donated by brethren of Structure Lodge No 5157 and the Mark Province of Hampshire and the Isle of Wight. A replacement carpet was sent by the Winchester Masonic Centre. The War Memorial had been taken, and consideration was given to replacing it with one commemorating brethren who made the supreme sacrifice in both World Wars. The Restoration committee had to report at the end of 1946 that they had abandoned a claim for damage and loss from the States of Jersey, because it had been announced that ex-gratia payments would only be made to business applicants. Seating had to be borrowed from the Theosophical Society, pending the construction of 100 new oak chairs. As part of the reinstatement of the property to Masonic control, a new company the Jersey Masonic Temple Company (1945) Ltd was created. They did not submit any accounts to Lodges for rent until 1947 when after some prompting from the Management committee, three years rent were requested at once.

After the Occupation, the best that could be procured for use at meetings, were three Windsor chairs. Before the sacking, the three chairs on the dais had dominated the room, the larger having been of particularly noble dimensions. The Immediate Past Master's chair had been made for RW.Bro J.J.Hammond, when he was Provincial Grand Master and bore his crest of a lion rampant. The other chair bore the unusual emblems of two serpents and a dove. It will be realised that three Windsor chairs were hardly a suitable replacement.

On the 4th November 1946, W.Bro Knocker was passing the doors of Deslandes Auction Rooms in Stopford Road. He noticed two old chairs of exquisite design and workmanship, which were to be auctioned later that day. They were in a poor state of repair, but were of such workmanship and quality that W.Bro Knocker returned to the Temple and instructed the caretaker, W.Bro R.O.Marquis to make a bid of up to £4 for the pair, which was successful. A maker's brass plate was found of the back of each chair bearing the inscription "T.O.Lyte, Jersey." It was later established that these had been constructed in 1842 for the Foresters Court of Prosperity who had used them up to the Occupation, but were now forced to remove to smaller premises disposing of their two "rulers'" chairs. T.O.Lyte was himself a local Freemason. They were renovated by Mr J Le Miere and Mr F.A.Morin, craftsmen working for A.de Gruchy & Co, and a third larger chair was commissioned to match the other two. The work was completed in 1948, the larger chair costing exactly £100.