WHITE PLAINS, N.Y. — While significant accounting charges related to the company’s portfolio restructuring and headquarters relocation dragged down financials, core business of Bunge Ltd. exceeded the company’s expectations for the third quarter, said Gregory A. Heckman, chief executive officer of the White Plains-based company.

“I don’t know that we could see a much more difficult environment than we’ve seen,” Mr. Heckman noted during an Oct. 30 conference call with analysts. “You can stack A.S.F. (African swine fever), the on-again/off-again trade war, the late harvest in the U.S. and then the Argentinian elections. And I couldn’t really be more pleased with the amount of change we’re driving through the organization and that the team continues to execute very, very well.”

Bunge sustained a loss of $1,496 million in the third quarter ended Sept. 30, which compared with income of $357 million in the third quarter a year ago, equal to $2.44 per share on the common stock.

Sales were $10,323 million, down 10% from $11,412 million.

Charges in the third quarter of fiscal 2019 included $1,603 million related to assets classified as held for sale in the Sugar & Bioenergy business (no charges in 2018); $107 million in impairment charges (no charges in 2018); $11 million in expired indemnification asset in Agribusiness (no charge in 2018); $8 million for severance, benefits and other costs ($7 million in 2017); and $1 million in sugar restructuring charges ($2 million in 2018). Overall, special charges totaled $1.7 billion in the third quarter of 2019, versus charges of $18 million in the third quarter of 2018.

“In Agribusiness, crush margins declined during the quarter, especially near the end of the period, and our grain business was impacted by ongoing trade issues and a delayed U.S. harvest,” Mr. Heckman said. “Nevertheless, our team did a great job in mitigating those challenges, and our results were positively impacted by our risk management actions. Results in Edible Oils were strong, reflecting favorable industry dynamics and good execution.

“… a lot of the noise in our results this quarter was connected to the strategic actions we are taking. In July, we announced our agreement with BP to contribute our Brazilian Sugar & Bioenergy business to a new 50-50 joint venture. As a result of this, we’ve reclassified that business as held for sale and taken the expected $1.6 billion charge we discussed on our last call.

“We remain very excited about the transaction and our new partnership with BP. It checks the boxes across all of our strategic criteria, reducing our exposure to Brazilian Sugar & Bioenergy, allowing us to strengthen our balance sheet and, importantly, enabling us to increase our focus on our core businesses. We’re on track to close the transaction before yearend, as planned.

“Also in the third quarter, we took a big step forward in our work to streamline our global business structure with the announcement that we’re moving our global headquarters to St. Louis where our North American headquarters is already located. This move will allow us to better align with our commercial teams and drive additional efficiencies with cost reductions as an additional output.”

Bunge’s largest division, Agribusiness, had EBIT in the third quarter of 2019 of $44 million, down sharply from $464 million in 2018. Agribusiness volumes were 36,554,000 tonnes, down 3% from 37,690,000 tonnes in the third quarter a year ago. Sales were $7,008 million, down 11% from $7,905 million in the third quarter of 2018.

John W. Neppl, chief financial officer, said during the call that Agribusiness results were adversely affected by approximately $70 million of mark-to-market reversals on soy crush contracts.

“Softseed processing results in the quarter were higher than last year, led by Canada and China, as were results in trading and distribution and biodiesel,” Mr. Neppl said. “In grains, results were lower in both North and South America, primarily due to soft export demand, farmer retention related to the U.S.-China trade dispute and the delayed harvest in the U.S. Results in ocean freight and trading and distribution were lower than last year.”

Providing more color on the challenges in Agribusiness, Mr. Heckman said the on-again/off-again trade war has “kind of been the worst of both worlds,” as the market struggles to adjust as if the trade war is over, when in reality it continues on.

“So it’s been about as confusing an environment as we could see,” he said. “And I think that, as we look toward ’20, it would be hard to imagine probably a more challenging or confusing environment than (what) we’ve seen the last 30 days.”

EBIT of the Bunge Edible Oil Products division was $52 million, up 73% from $30 million in the third quarter of 2018. Sales were $2,319 million, up narrowly from $2,298 million.

Mr. Neppl said Edible Oil results were driven largely by better results in North America and Brazil, benefiting from better supply/demand balance of soy oil as well as improved execution.

EBIT of the Milling Products division totaled $7 million in the third quarter of 2019, down 76% from $30 million a year ago. Net sales increased to $437 million from $427 million.

Weaker Milling results reflected lower margins in the United States and lower volumes and margins in Mexico, Mr. Neppl said.

Mr. Neppl said capital expenditure spending totaled $378 million in the first nine months of fiscal 2019, which compared with $318 million in the first nine months of fiscal 2018. For the full year, capital expenditures are expected to total $520 million to $540 million, he said, with approximately $115 million of that total related to the sugarcane milling business.