Though they had been doing well enough in the depression to purchase a two story factory in 1934, with World War II came supply shortages like the ones which had put the original producer of Fluff out of business. The existing sugar supply was rationed to the corporations that needed it. Unwilling to stretch their supplies by altering the recipes of Fluff and Sweeco, which would have lowered their quality, Durkee-Mower was forced to cut production back considerably. In the interest of fairness, they allotted their products to the distributors on a percentage basis, each distributor's quota determined by their pre-war sales records. During this period, the company's resources were used to promote the war effort in various ways. Part of the factory was converted to wrap war critical electronic and optical parts in special water proof packages. Some of their advertising helped promote victory gardens in cooperation with the Massachusetts State War Garden Committee. With little Fluff to sell, the Flufferettes show threw its advertising support to the armed forces, particularly the Navy, the branch which Allen Durkee's two older sons served during the war years.

Meanwhile Durkee-Mower worked on plans for the future. In 1945 they built a new modern office building adjacent to the factory purchased eleven years earlier. When industrial sugar rationing ended in 1947 the company was preparing for another expansion. They started by redesigning the product's package. A survey covering a wide sample of New England housewives told them that the experts, their customers, thought that the best jar for Fluff would be short enough to fit easily into the refrigerator to be used for leftovers (Fluff requires no refrigeration), and have a wide enough opening to fit a tablespoon into. In addition, the jar was made with a stippled surface above and below the label to make it stronger and more easily gripped. The jar's longevity in a rapidly changing market is a tribute to its success; the same basic jar is still in use today.

Having designed the jar, Durkee-Mower designed the factory that would fill those jars with Fluff with the greatest efficiency. When the new factory opened in 1950, it was one of the most modern food manufacturing plants in the country. Much of the machinery was specially designed for Durkee-Mower. The new filling and capping machines increased the speed of production from 80 jars per minute to 125. Much of the line was automated, but because their plans included increasing production, they could automate without laying off any employees. Speed and efficiency however came second to cleanliness and purity. Wherever Marshmallow Fluff was exposed to air the room was air conditioned or dehumidified or both. The walls and floor were sanitary tile covered to facilitate the daily wash down which still takes the crew one and a half hours to complete. They switched from using granular sugar in 100 pound bags to liquid sugar stored in 5500 gallon stainless steel tanks. Every conceivable measure is taken to protect the purity of Marshmallow Fluff. Because of the sanitary environment and practices it is not necessary to refrigerate Marshmallow Fluff even though it still contains no preservative of any kind.

In 1956 the company collaborated with Nestle in a nationwide ad campaign that won the Promotion-of-the-Year Award. They printed a recipe for fudge in Ladies Home Journal and other magazines. The fudge was quick and easy to make, and included Fluff and Nestle's Chocolate Bits. The same recipe can still be found on the backs of Fluff labels and in the Recipe Book.