Lyard, 36, from Marcenais, was third after dressage on Jessy Mail, whom he rode in the CIC at Aachen and was 21st at Saumur CCI*** in May.
He steadily moved up after the dressage runner-up Eddy Sans was eliminated on the cross-country on Kramique, and then the overnight leader, Britain's Pippa Funnell, hit one show jump on Ensign.
With Martinvast coming straight after the Olympics, only two riders managed to turn themselves around after Hong Kong to get there, team silver medallist Clayton Fredericks (Australia) on Poilu, 11th, and New Zealand's Joe Meyer, 22nd on his Burghley entrant Ariki.
Nonetheless, it was still a highly impressive field which started at this popular event, with 50 riders from 12 nations. Zara Phillips (GBR), the world champion, was ninth with Red Baron and 10th with her new ride, Tallyho Sambucca, who is entered for Blenheim CCI***.
Pippa Funnell, who has been absent from British teams since winning Olympic team silver and individual bronze in 2004, was paying her first visit to Martinvast. As well as finishing second on Ensign, with whom she might contest the HSBC FEI World Cup Final at Deauville (September 18-21) and the fifth and final leg of the HSBC FEI Classics in Pau CCI**** (France), where they finished third last year, she was third on Blue Horizon, who is entered for Blenheim CCI***.
"I loved it," she said. "It was a brilliant event. It helped that the cross-country going was beautiful, but there were very good tracks which rode well and the organisation was so friendly. It also struck me how hard the fence judges worked; they were always raking the take-offs and landings."
Thirty-eight riders finished the competition, but only one achieved the optimum cross-country time, Italian show jumper Juan Carlos Gracia, riding the former French horse Iman du Golfe, fourth.
Marie-Christine de Lauriere, who rode for France at the Atlanta Olympics in 1996, was fifth on Cadiz, and former World Champion Jean Teulere (FRA) had some compensation for missing the Olympics when finishing sixth on Matelot du Grand Val.