The maker of Nescafe drinks and Purina pet food said in a statement the dismissal was effective immediately.
An investigation found the undisclosed romantic relationship with an employee violated Nestle's code of conduct.
Freixe, who had been chief executive for a year, will be replaced by Philipp Navratil, a long-time Nestle executive.
"This was a necessary decision," said chairman Paul Bulcke.
"Nestle's values and governance are strong foundations of our company."
The company did not give any other details about the investigation.
Freixe had been with Nestle since 1986, holding roles around the world.
When the company revamped its geographic structure in January 2022, Freixe became chief executive of Zone Latin America.
In August 2024, he was tapped to replace then-chief executive Mark Schneider in the top role, and started September 1, 2024.
Navratil started his career with Nestle in 2001 as an internal auditor and served in a variety of roles in Central America.
In 2020, he joined Nestle's Coffee Strategic Business Unit, and in 2024, he became chief executive of Nestle's Nespresso division.
It is the latest in a string of personnel changes for the company.
In June, Bulcke, a former chief executive who has been chairman of the board since 2017, said he would not stand for re-election in 2026.
In April, Steve Presley, an executive vice president and chief executive of Zone Americas, said he was retiring after almost 30 years of service.
Based in Vevey, Switzerland, Nestle has been facing headwinds like other food makers, including rising commodity costs and the negative impact of US tariffs.
It said in July it offset higher coffee and cocoa-related costs with price increases.
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