Viktor and Amalija Knavs, both in their 70s, took the citizenship oath at a private ceremony in New York City.
Michael Wildes, the couple's immigration lawyer, confirmed they took the oath of citizenship on Thursday.
Asked about President Trump's heavy rebuke of family-based migration, Wildes said: "I can't comment on the President's politics when it comes to my clients but I have stood up against the President's immigration policies personally".
In a Tweet last November, Trump slammed CHAIN MIGRATION or bringing families into the USA, calling it truly evil.
"CHAIN MIGRATION must end now!" he tweeted.
When Trump began her modelling career, while still a teenager, the whole family sensed opportunity, according to those who knew them in Slovenia.
Under immigration statutes, the Knavses would have needed to have their green cards for at least five years in order to apply for citizenship, along with fulfilling character, residency and civic knowledge requirements, it said.
The couple was escorted to and from the Manhattan ceremony by Homeland Security police.
The Knavses' lawyer said they had "travailed a wonderful journey".
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According to the US Citizenship and Immigration Services website, an average naturalisation application in NY takes between 11 and 21 months and is dependent on numerous character and residency requirements.
The ceremony has prompted questions about Donald Trump's flagrant disregard for practising what he preaches, as the First Lady's parents obtained citizenship through a policy he has vocally denounced. Experts estimate that could cut overall immigration to the United States by 40% to 50%, if those green cards are not reallocated to another category.
The Knavses' citizenship ceremony was kept hush-hush around the Jacob K Javits Federal Building.
According to news reports, she entered the country in 2001 on a so-called Einstein visa for "individuals of extraordinary ability" as a model.
Melania Trump, who has been vacationing with her husband in Bedminster, New Jersey, did not accompany her parents.
The couple met in Sevnica, Slovenia in 1966, and Melania was born in the same town.
Mr Knavs was a auto dealer while Ms Knavs worked in a textile factory.
Viktor is 74, two years older than President Donald Trump. Now, we're certain his shameless hypocrisy sees no boundaries.