The professor, Daniel Kammen, included a less-than-subtle assessment of Trump in his resignation letter by spelling out the word "impeach" with the first letters of each paragraph.
"My view on impeachment is perhaps less formal than if I was an elected member of Congress," Kammen said in an interview with CNN, "but I don't view what the President is doing as consistent with the best interests of the United States and the global community."
The subliminal message was also meant as an homage to a similar letter penned earlier this month by the Committee on the Arts and The Humanities in which the first letters of each paragraph spelled out the word "resist."
Kammen published his full resignation letter in a tweet Wednesday morning, writing, "Mr. President, I am resigning as Science Envoy. Your response to Charlottesville enables racism, sexism, & harms our country and planet."
He told CNN he had grown increasingly frustrated with the administration over its environmental and regulatory policies, as well Trump's decision to pull out of the landmark Paris climate agreement. But it was the President's remarks last week on the violence in Charlottesville that spurred him to write the letter.
Kammen, who is white but married to a Nigerian-American woman with whom he has biracial children, said the incident was a turning point for him.
"I can't stand with this President and then go home and tell my kids, 'Gee, I'm working with someone who seems to be promoting neo-Nazis, racism, sexism,'" he said.
"It was sadly easy to step down because I view what the President is saying as inconsistent with what's in the best interests of the country and my mandate as science envoy," said Kammen. "But it was hard to step down because I really value the relationships with the individuals (at the State Department) and the relationships with these foreign governments, and I don't want to step away from that."
The State Department's website still lists Kammen as one of seven science envoys, and notes that his focus area is "building capacity for renewable energies." It is not a paid or full-time position, but does involve agency-funded travel to promote science initiatives the US considers to be strategic priorities.
Kammen, who was appointed under former President Barack Obama, says he primarily worked on projects in Africa and the Middle East during his time in the position.
He also chairs the UC-Berkeley Energy and Resources Group, according to the school's website, and has served on several government advisory panels. He hosted the Discovery Channel miniseries "Ecopolis" in 2008.
Despite his frustration with the White House, Kammen insists he's not disheartened.
"I'm disappointed in this administration," he told CNN, "but I would say the actions that made the Paris Accord happen have never been stronger."
He plans to continue working on energy projects with the state of California and foreign governments, he added. "It's just, in my view, not possible to work with the White House right now."
A State Department official confirmed Kammen's departure.
"Today, Dr. Daniel Kammen made a personal decision to resign," the official said. "We appreciate his dedicated service to U.S. scientific diplomacy during his appointment working on energy efficiency and renewable energy in Africa as a science envoy."