According to the Times, Mr Trump's 15 golf courses have lost $315.6m over the past two decades.
Mr Trump's largest golf resort, the Trump National Doral in Miami, Florida, faces a $125m mortgage due in three years. The president bought the Doral in 2012 for $150m, and proceeded to lose $162.3m on the property.
The president's European properties did not fare much better; the three golf resorts have seen $63.6m in losses since he took possession.
Despite the overall losses, the presidency seems to have helped Mr Trump generate revenue at his clubs.
Membership at Mr Trump's Mar-a-Lago resort spiked after he announced his plans to run for president. Between 2015 and 2018, Mr Trump took $26m out of the club, which is nearly triple what he took in previous years.
The president is currently under investigation in New York by state Attorney General Letitia James regarding one of his golf properties. Investigators are examining whether Mr Trump illegally inflated the value of his property, the Trump National Golf Club.
The Los Angeles location is not the only one of Mr Trump's properties raising eyebrows.
The New York Times investigation found that the administrative expenses Mr Trump claimed for his golf property in New Jersey was five times higher in 2017 than it was in 2016. There was no immediate explanation for the reported increase, which Mr Trump then used to reduce his overall taxable income.
According to the report, the president has only paid $750 in federal taxes in 2016 and 2017, and may owe the IRS more than $100m if his claimed businesses losses are deemed illegitimate.
The president has been embroiled with the IRS for years. In 2010, he won a $72.9m refund from the tax agency.
Mr Trump has predictably dismissed the claims made in the Times article as "fake news".
"The Fake News Media, just like Election time 2016, is bringing up my Taxes & all sorts of other nonsense with illegally obtained information & only bad intent. I paid many millions of dollars in taxes but was entitled, like everyone else, to depreciation & tax credits..." he wrote at the start of a series of tweets on Monday.
Democrats have already pounced on the story. Democratic presidential challenger Joe Biden's campaign has already produced an ad calling attention to the tax story, comparing Mr Trump's tax payments to those made by average nurses, firefighters and teachers.