The One Show host, 45, revealed that she locked the then-future monarch in a toilet during her first job as a researcher for a TV production company.
King Charles, then Prince of Wales, was leading an opening ceremony for a new grant the company received to give young people in disadvantaged areas of Wales opportunities to work in the media.
The former Shop Well For Less? presenter said she knew the river next to the building "had a bit of a stench to it" that came through the window in the men’s toilet.
Jones took the initiative to lock the door so that the royal couldn’t smell it. Then, rather mysteriously, the special guest was nowhere to be found.
“There was this massive sense of panic and they were like we don’t know where he is,” she explained. “Prince Charles has actually disappeared.”
“And I was like ‘there must be an aide or something that knows where he is’ and they were like ‘no we can’t find him either’ and I was like ‘oh weird,’” she told author Elizabeth Day on the How to Fail podcast.
Jones said she then heard someone knocking from inside the men’s toilet, realising where the Prince had disappeared to.
Jones said he was “lovely” and “saw the funny side” to the accident.
The pair later reunited when King Charles, then Prince of Wales, met young people involved in social action via his first ever Google Plus Hangout as part of the #iwill campaign at Clarence House in 2014. Jones presented the webinar.
The TV host also revealed other mishaps in her early career. One incident involved losing the cello of conductor and composer Julian Lloyd Webber, who was “furious”.
“He’s got brilliant eyebrows but they were going at a million miles per hour he was so cross and rightly so.”
Recalling how she got into presenting, Jones revealed she was fired twice but “just kept going back on the Monday”.
Jones is presenting a new documentary titled Alex Jones: Making Babies that was released on Thursday 5 January on W channel. In it, Jones trains as a fertility assistant at one of the UK’s leading fertility clinics, where she is taught how world-renowned embryonic technology works.
Elsewhere in the podcast, the presenter opened up about her miscarriage in 2017; she had her first child aged 39.
Jones has three children; Teddy, five, Kit, three, and Annie, one, with husband Charlie Thomson.
She said her own experiences with struggling to conceive had informed her role in the new documentary.
“I know all about the complications,” she said.
“But at least I’ve got a plan B now,” she joked, referring to her recently learnt skills as a fertility assistant.