He began the season by straining his hamstring during practice four days before the season opener. However, he still started against the Falcons, but aggravated his hamstring in the second quarter and sat out remainder of half before coming back for the second half as offense recorded 403 total yards. He played at the New York Giants on September 15, and helped protect Quincy Carter, allowing him to throw for 321 yards in leading Dallas to a come-from-behind overtime win. He suffered a sprained left knee in the second quarter against the Cardinals on October 5, but returned in the second half to help Dallas total 365 yards of offense. Despite playing sporadically against the Washington on November 2, due to a sprained left knee suffered in the first quarter, he helped the Cowboys record 400 yards of total offense, including 208 rushing yards. Allen also helped hold DT Kris Jenkins to zero sacks, while the Dallas line allowed only one sack for zero yards in 45 pass plays against the Panthers on November 23. He also helped lead way for Troy Hambrick to run for 189 yards against the Redskins on December 14.