For 2006, Almirola drove the No. 75 Spears Manufacturing Chevy for Spears Motorsports in the Craftsman Truck Series, as part of the JGR development program. He started every race and had three top-ten finishes, including a best finish of ninth, ending the season 18th.
That season, he also drove nine races in the Busch Series for Gibbs in the No. 19 Husqvarna/Banquet Foods Chevrolet Monte Carlo. His best finish was an eleventh at Dover International Speedway.
He also served as a test driver for Gibbs teammates J. J. Yeley and Denny Hamlin when their Nextel Cup and Busch Series schedules conflicted. He also scored his first career pole at the Milwaukee Mile, qualifying the No. 20 car for Denny Hamlin, who competed in the race.
Almirola moved up to the Busch series on a regular basis in 2007, driving the No. 18 and No. 20 Chevys for Joe Gibbs, driving each car in ten races apiece. He won his second career pole award for the Orbitz 300 at Daytona. He won the pole again, for the second straight year, at the Milwaukee Mile, but thought he was going to give up driving duties to Hamlin again; Hamlin's helicopter was unable to land in time for Hamilin to make it to the track, so Almirola started the race, leading the first 43 laps of the race.
On lap 59, during a caution period, because of sponsor commitments, Hamlin took over for Almirola while he was running in the third place.
Hamlin went on to win the race, but Almirola was credited with his first NASCAR Busch Series win because he was the driver who started the race. Almirola did not participate in team victory celebrations after the race as he had already left the track.
He asked for, and was granted his release from Joe Gibbs Racing a month later. He soon joined Dale Earnhardt, Inc. following the sale of Ginn Racing. He drove the No. 01 Chevrolet in five races in 2007, and had a best finish of thirtieth.