The Scot, who began the week with two rounds of 70, picked up six birdies against two bogeys on a tidy tour of the Parador de El Saler Golf Club.
Warren's nearest challenger is compatriot Craig Lee, while David Horsey and Paul Waring lie a further stroke back. American Peter Uihlein, the overnight leader fell back after a two-over-par 74.
“I am very pleased with today’s work,” Warren said. “They were tough conditions on a tough golf course so to shoot 68 is a very pleasing day.
“I like the fact you’ve got to hit so many different shots (in the wind). There was always something to the shots today and I felt as if I did well today. Hopefully that continues tomorrow.
“Concentration is paramount, especially on a course as tough as this one, and it will be tomorrow.”