Turbulence in the retail sector is hitting executives working for the top mall companies where it hurts: in their wallets.

Senior management teams at the country’s largest mall owners, including Simon Property Group Inc., GGP Inc. and Macerich, are taking cuts to their compensation as they navigate an industry beset with struggling retailers and increasing competition from online shopping.

The slide in compensation among retail landlords is unusual in the corporate world. Executives at companies in other sectors are less likely to feel the pain of a rough patch because their pay isn’t as closely tied to stock performance.

But the real-estate investment trust industry is ahead of most other sectors in designing pay plans to align the interests of shareholders and management, according to according to Jeremy Banoff, a senior managing director with FPL Associates LP, a compensation-consulting firm that focuses on the real-estate industry.

As a result, when stocks fall, it is more likely that compensation cuts result, he said. “The rest of the world is playing catch-up,” Mr. Banoff said.

Indianapolis-based Simon, the country’s largest mall owner with stakes in more than 325 properties, took the rare step of eliminating stock grants tied to the company’s long-term performance for top executives, according to its proxy statement filed with the Securities and Exchange Commission.

Simon did this because of “the challenging business conditions in the retail industry that the company is facing,” according to the proxy statement. A spokeswoman for Simon declined to comment beyond what was written in the filing.

Executives at other big mall owners suffered because their compensation is tied to the performance of their share prices, which have been hammered during the past 18 months as investors have fled the sector.

For example, Macerich chief executive Arthur Coppola had a target compensation package — including base salary, annual incentive and other benefits — potentially worth $12 million in 2016. But because the company’s stock price dropped, Mr. Coppola was on track to receive only $5.7 million of that, according to the company’s proxy filing.

“That’s the way the stock plans are structured,” said Macerich Chief Financial Officer Thomas O’Hern in an interview. “When the stock is down, we suffer from a compensation standpoint.”

The retail sector was facing problems even before the e-commerce revolution. Rampant development left the U.S. with far more malls than it needed by the time the last recession hit.

A decade later the country is still…