By Tom Fairless 

BRUSSELS-- Starbucks Corp. is going through the grinder in Europe.

The world's biggest coffee chain has raised suspicions among regulators and local governments by reporting losses in its biggest European markets for years despite recording hundreds of millions of dollars of annual sales.

Last year, as European Union regulators opened a formal investigation, a profit materialized: EUR407 million ($446.6 million), reported by the company's European head office in Amsterdam. The coffee chain has since moved its headquarters to London.

The reason for the windfall: 502 million Swiss francs ($527.8 million) in dividends, transferred from the company's coffee-buying unit in Switzerland, which has fewer than 40 employees, according to corporate filings.

The huge profit is likely to stoke concerns around Starbucks's tax practices in Europe, which are under scrutiny for the second time in just over two years. EU antitrust chief Margrethe Vestager, who is running the bloc's investigation of Starbucks's tax affairs, has pledged to announce results by June, which could include sizable back-tax demands.

Starbucks has long insisted that its complex European structure--which until recently centered in the Netherlands rather than the U.K., by far its biggest market in the region--wasn't designed to avoid tax. The structure, it said, was built around its Amsterdam-based coffee-roasting house and reflected that city's rich history with coffee.

Even so, the tax advantages are clear: The Amsterdam unit paid just EUR2.6 million in corporate tax on last year's EUR407 million pretax profit in the Netherlands--or well under 1%--as part of a deal with the Dutch government that has drawn the attention of EU regulators.

All the coffee Starbucks uses world-wide is bought by the company's Swiss unit, even though the coffee never actually transits through Switzerland. It is then sold to Starbucks operations around the world at a 20% markup, the company's former chief financial officer, Troy Alstead, told British lawmakers in 2012, after Starbucks found itself at the center of a controversy over its tax bills.

That means the Swiss unit loads costs onto the coffee bought by Starbucks stores around the world and depresses their profits. British lawmakers have expressed skepticism that the 20% markup was "reasonable."

Starbucks said that "profits generated by [its] companies are periodically paid as dividends," and that it follows international guidelines in charging fees between business units in different countries.

On the same day the Swiss dividends arrived in Amsterdam last October, Starbucks transferred the bulk of them to a new U.K. holding company--one of three British entities it has created since June--corporate filings show. It subsequently dissolved another London-based shell company, Alki LP, which had become a focus of EU regulators' inquiries because it received tens of millions of dollars annually in royalty payments from Amsterdam.

Starbucks is one of four multinational companies operating in Europe--along with Apple Inc., Amazon.com Inc. and Fiat Chrysler Automobiles NV--whose tax affairs are being investigated by regulators in Brussels.

Above all, Starbucks stands out for its response: Rather than citing a duty to investors to minimize tax, as other companies like Google Inc. have done, Starbucks has repeatedly pleaded innocent.

"We do nothing--nothing--to avoid taxes," Mr. Alstead told British lawmakers in 2012.

Now, that narrative is being challenged.

In a preliminary decision in November, EU regulators argued that Starbucks's structure in the Netherlands had no economic rationale. Their probe could result in a back-tax bill running into tens of millions of dollars. Dutch regulators have said they believe Starbucks's structure in the country is appropriate.

Tax avoidance isn't illegal. Other companies like Google and Facebook Inc. minimize their taxes by moving foreign profits through countries such as Ireland, the Netherlands and Bermuda.

Starbucks said it complies "with all relevant tax rules, laws, and...guidelines" and pays "a global effective tax rate of 34 per cent." The coffee chain gets about three-quarters of its revenue in the U.S., where the top marginal corporate tax rate is 35%, adding to state and local corporate taxes.

But the EU has found a new way to clamp down on corporate tax avoidance using a law that prohibits sweetheart deals that allowed some companies to pay less tax than others. This led it to also investigate the tax affairs of Apple, Amazon and Fiat. All three companies have denied receiving special treatment, and the national governments involved have denied giving it. The EU has said it plans to publish results of its probes by June.

At the center of the probe is a web of partnerships operated by Starbucks in the Netherlands and the U.K. Two of the partnerships--Rain City and Emerald City, nicknames for its Seattle hometown--are based in the Netherlands but aren't subject to Dutch corporate tax, according to the EU's report and corporate filings.

Emerald City owns a Hong Kong-based vehicle that controls Starbucks's operations in Beijing and northern China and the company's 50% stake in its Indian joint venture. It also owned a third, now-dissolved European partnership, Alki, which was based in London.

EU regulators have homed in on Alki, which held all of Starbucks's intellectual-property rights for Europe, the Middle East and Africa--and received tens of millions of dollars in annual royalty payments from Amsterdam. Hefty royalty payments to units in lower-tax jurisdictions are another tool that multinationals can use to avoid tax.

In a preliminary decision in November, the European Commission questioned royalty payments made by Starbucks's manufacturing unit to Alki, which didn't pay Dutch corporate tax. It is unclear whether the holding company, which was based in the U.K. before it was dissolved, paid U.K. taxes.

Starbucks declined to comment on Alki's tax treatment. In its report, the commission said royalty payments to Alki from Amsterdam were considered a direct payment to Starbucks's U.S. operations from a Dutch tax perspective. The commission also said the royalty didn't "reflect the value of the intellectual property" because it "fluctuates from year to year and is not in line with sales."

The Dutch government said it was "convinced" that its tax deal with Starbucks didn't constitute illegal state aid.

Alki was dissolved last December, shortly after its ownership was transferred to a new U.K. company, Starbucks EMEA Holdings Ltd., according to corporate filings. Starbucks announced last year it would move its regional headquarters to the U.K. from the Netherlands. "This structure [Alki] no longer exists," it said in a statement.

Alki had no employees, a person familiar with the matter said. Its address in London was the U.K. headquarters of Baker & McKenzie, a law firm that advises Starbucks on tax matters. Starbucks and Baker & McKenzie declined to comment on the matter.

The EU investigation comes after a tax furor in Britain led to store boycotts and a 2012 parliamentary hearing. The company's U.K. annual sales fell following the furor, its first decline since it set up shop in the country in 1998.

At the time, Starbucks had paid GBP8.6 million ($12.8 million) of British corporate tax over 15 years despite sales exceeding GBP3.5 billion in Britain. It has since voluntarily paid an additional GBP20 million by forgoing certain deductions.

At the hearing, Mr. Alstead, who previously served as a director of the U.K. business, blamed the company's persistent losses in Britain on "strategic mistakes," including expensive property leases. "We are not at all pleased about our financial performance here," he said.

British lawmakers weren't convinced. "If you have made losses in the U.K. over 15 years, which is what you are filing, why on earth are you doing business here?" said Margaret Hodge, who chaired the hearing. "It just doesn't ring true."

According to corporate filings, Starbucks's British business started making large royalty and license-fee payments to Amsterdam in 2003, five years after it opened in the U.K. Mr. Alstead last month took unpaid leave after 23 years with the company "to spend more time with his family," Starbucks said. It said his decision to take time off was a personal one, unrelated to the corporate structure.

British lawmakers are no longer investigating Starbucks.In Britain, Starbucks recently reported its first annual pretax profit: GBP1 million on sales of GBP409 million in the year to September. But after years of deep losses, the company has accumulated GBP35 million of deferred tax assets that can be used to offset future tax bills. That indicates it won't have to pay any U.K. corporate tax for some time.

Starbucks said that the U.K. business "is now profitable and as our turnaround continues, our tax payments will increase in line with our profits."

Write to Tom Fairless at tom.fairless@wsj.com

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