When customers began to line up at 5 a.m. outside Scott Metzger’s microbrewery in San Antonio, Mr. Metzger knew he had to start making more beer.

Mr. Metzger, who founded Freetail Brewing Company as a brew pub about seven years ago, spent thousands on new equipment so that he could start canning Soul Doubt, his signature India pale ale; Bat Outta Helles, his Bavarian-style lager; and a number of seasonal flavors and other brews. Now, there’s just one unexpected problem: Where will he get the cans?

While the craft beer boom has benefited small breweries around the country, it has also left some scrambling for cans. The 16-ounce size is in exceptionally high demand; it’s slightly larger and has become a popular way for niche brewers to distinguish themselves from behemoths like Budweiser and Coors, which use 12-ounce cans.

“Certainly we’ve seen some of our brewery members struggle in recent months,” said Bart Watson, the chief economist at the Brewers Association, a national trade group for craft beer businesses. “This has proven to be a real challenge for members that have built their business model around getting these cans.”