Schools are struggling to secure food for student breakfasts and lunches ahead of classrooms’ planned reopening in the fall.

Some cafeterias are cutting menu choices as food suppliers face labor shortages and transportation challenges that are adding costs and limiting supplies. Food distributors and school officials say they expect to run low on everything from canned fruit to lunch trays, and some worry that the lack of options will deter students from getting meals at school.

Across the country, school cafeterias are preparing to welcome back students after running hybrid or remote learning operations for much of the past school year, when they offered prepackaged or to-go food. Many now find themselves at the center of supply-chain woes gripping the broader food industry: Manufacturers are cutting flavors or halting production because of capacity problems, while some distributors dropped deliveries to schools. Some school districts are struggling to hire cooks.

“We haven’t had a 100% head count school season in 15 months. It’s going to blow the doors open,” said Andy Mercier, chief executive at Merchants Foodservice, a distributor that serves K-12 schools in Alabama and Mississippi.

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Corn dogs, hamburger beef patties and other items that require more hands-on labor are hard to come by, Mr. Mercier said, because manufacturers are short-handed. A salsa supplier recently told his company that it doesn’t have enough workers to produce sauces for schools. Merchants Foodservice is itself running low on lunch trays as manufacturers give priority to takeout trays for restaurants, he said.

Rising transportation costs, labor pressure and ingredient constraints have squeezed U.S. food makers and sellers for months, as the U.S. economy rebounds from the Covid-19 pandemic and restaurants reopen for in-person dining. Such challenges are acute for schools that have to meet U.S. Department of Agriculture requirements for nutritional value and packaging sizes, industry officials said.

The federal agency has given leeway to schools during the pandemic. The USDA is offering free meals to students, allowing parents to pick up food when meal programs are closed, and waiving some nutritional requirements such as sodium and grain levels. Many changes are staying in place through June 2022, but some schools, manufacturers and distributors say their supply-chain issues are worse today than last spring, when Covid-19’s fallout broadly disrupted the U.S. food industry.

National Food Group secures apples from Washington, Michigan and New York, producing about 1.5 million cases of applesauce a year.

National Food Group secures apples from Washington, Michigan and New York, producing about 1.5 million cases of applesauce a year.

Photo: National Food Group

“These are some of the most challenging times we’ve had in the current generation,” said Priscilla Riedel-Cohan, program coordinator for school nutrition at Arch Ford Education Service Cooperative, which consults and buys food for K-12 schools in central Arkansas.

Arch Ford is revamping some operations and studying ways to speed up the distribution process. It is simplifying menus by using chicken, pasta and other staples in a variety of ways so that distributors don’t have to stock as many items, Ms. Riedel-Cohan said.

She is advising schools to consolidate deliveries and make faster payments to appeal to more vendors. Ms. Riedel-Cohan is also finding new suppliers of items like fresh bread after Harris Baking Co., a major supplier, said it wouldn’t produce for schools during the coming academic year because of limited production capacity and a driver shortage.

The USDA’s Food and Nutrition Service said it is focused on helping ease pressures across the food supply chain. While there have been some shortfalls in various products, no widespread concerns have been identified, it said, adding that it continues to provide updates to states about any procurement challenges. The agency said it is committed to ensuring that children have nutrition they need and supporting school food operators.

Manufacturers are trying to meet demand. National Food Group Inc., a maker of snacks for schools, is reducing its flavors of Zee Zees applesauce by nearly half to cut the number of ingredients the company needs to buy, President Sean Zecman said. The Michigan- and California-based company is stockpiling fruits like pears while it can before they become tougher to secure. That is a gamble, Mr. Zecman said, because his school customers don’t yet know how much inventory they want.

Other distributors said they can adjust and cope. Sodexo’s North America business is modifying menus to incorporate more widely available ingredients, and it doesn’t anticipate major disruptions, said Aaron LaMotte, its vice president of supply management.

“We do this every year regardless of whether we’re in a pandemic or not,” Mr. LaMotte said.

National Food Group is cutting its flavors of applesauce by nearly half to reduce the number of ingredients it needs to buy.

National Food Group is cutting its flavors of applesauce by nearly half to reduce the number of ingredients it needs to buy.

Photo: National Food Group

Some distributors are downsizing their education business, leaving schools to find new avenues for food. US Foods Holding Corp. recently notified some districts in Florida, Kansas and other states that it wouldn’t be serving meal programs for the coming school year. Nonprofit group School Nutrition Association wrote in a letter last month to Agriculture Secretary Tom Vilsack that the exit was because of the distributor’s labor shortages and insufficient warehouse capacity.

US Foods said labor challenges weren’t a factor, and that its decision to pull back from servicing some schools was specific to individual districts. The USDA said it is in regular contact with SNA.

Oklahoma’s Moore Public School District joined a state cooperative after US Foods alerted officials that it wouldn’t be delivering food this academic year, said Pam Hart, the district’s child nutrition director. US Foods typically handled about half of the district’s food.

Ms. Hart said the district still expects shortages in popular items like J.M. Smucker Co. ’s Uncrustables sandwiches and Italian salad dressing. Moore’s schools are planning to pare down menus as they work to fill cafeteria staff, and Ms. Hart said students likely will feel the impact.

“It’s a no-win situation. They will bring their lunch or go out to eat,” she said.

Write to Jaewon Kang at jaewon.kang@wsj.com