The top two finishers at the MARS Badminton Horse Trials both had flag penalties which caused concern, but were later dropped.
The Olympic gold medallist squeaked ahead of yesterday's leader Tom McEwen and JL Dublin with 21.1pp in the dressage phase.
Organizers are currently seeking a new title sponsor for the series which includes Kentucky, Badminton and Burghley three-day events.
Tim Price and William Fox-Pitt, leaders after cross-country, both had disastrous jumping rounds; Canada's Jessica Phoenix and Wabbit finish 30th.
Camilla will be on hand on stadium jumping day, May 12, to present prizes to the winners at this British eventing fixture.
The British rider is in the running to become only the third rider ever to capture the series at Mars Badminton Horse Trials next week.
A starting lineup of 90 entries – including Canada's Jessica Phoenix and Wabbit – is set to compete for record first prize money.
Prize money is now £425,000 for this CCI5*, part of the Rolex Grand Slam of Eventing and celebrating its 75th anniversary in 2024.