As the point person at the White House for bilateral relations, adviser, and President Donald Trump’s son-in-law Mr Kushner was there to do damage control after a phone call between Mr Trump and Mr Pena Nieto two weeks went badly.
Tensions rose as the proposed border wall and the North American Free Trade Agreement (Nafta) were discussed on the call, which took place just days after the US Ambassador Roberta Jacobson announced her departure.
Mr Pena Nieto cancelled his visit to the US as a result, according to two officials who had spoken to ABC News.
Mr Kushner also just lost his Top Secret security clearance, having been downgraded to the Secret level due to a series of errors and omissions on his paperwork.
Ms Jacobson, an appointee of former President Barack Obama, has been in the position for a little under two years and her resignation comes in the wake of several US State Department and Trump administration departures.
According to the New York Times, she was not even invited to Mr Kushner’s meetings with Mexican Foreign Secretary Luis Videgaray.
Ms Jacobson “was one of the most experienced Latin America experts in the State Department, having spent most of her 31 years there focusing on the region,” the newspaper reported.
Former State Department spokesperson John Kirby tweeted his criticism of Mr Kushner leaving Ms Jacobson out, despite her upcoming departure.
Mr Kushner has no diplomatic or political experience, worrying many Washington insiders and Mr Kirby likened the move to “diplomatic malpractice”.
President of the Council on Foreign Relations and former George W Bush administration staffer Richard Haas tweeted that it was “truly inappropriate” and “part of a larger pattern of undercutting our professional diplomats around the world that [Secretary of State Rex Tillerson] should not stand for”.
The ministry issued a short statement saying that Mr Kushner had discussed issues such as the fight against drug trafficking, border security, migration, jobs and Central America with his Mexican counterparts.
It made no mention of the border wall or how progress might be measured.
The issue of the wall has been a contentious one since Mr Trump began repeating the mantra on the campaign trail. He said in 2015: "When Mexico sends its people, they're not sending their best. They're sending people that have lots of problems… They're bringing drugs. They're bringing crime. They're rapists".
The Trump administration also tied wall construction to a negotiations on bill on the Deferred Action for Childhood Arrivals (Daca) programme, which is intended to protect those brought into the US illegally while they were minors from deportation.
The Trump administration also asked for $18bn (£13bn) over the next decade, for the initial phase of the border wall - significantly more than Mr Trump’s initial cost estimate of around $10bn.
Spirits briefly improved during Mr Kushner's trip when the White House said it might exempt Mexico and Canada from Mr Trump's planned tariffs on steel and aluminium, an idea he has floated as a trade-off in return for progress on Nafta.
Withdrawing from the trade agreement between Canada, Mexico, and the US was one of Mr Trump's key promises on the campaign trail in 2016. He claimed it is a "job killer" and was antithetical to his "America First" approach to foreign policy.
The deal, one of the largest trade agreement in the world, was originally signed in 1994 by President Bill Clinton and allows free trade between the three countries in North America.
According to the CBC News in October 2017, a source told them the US delegation at the round of negotiations on reforming the deal have been “uncomfortable with the demands they are presenting, which appear to have been dictated to them by the Trump administration.”
The seventh round of Nafta negotiations ended earlier this week in Mexico City and one official told Reuters Mr Kushner pushed for a “speedy” renegotiation.