Barnet were now an Alliance Premier League Club and in 1979-80, the club had their best run in the tournament since they reached the final in 1972. They were drawn at home to fellow APL club, Wealdstone in the 1st Qualifying Round and the match ended goalless. The replay was drawn too, this time 1-1 with Steve Turner scoring the Barnet goal. The 2nd replay was held at Underhill and the Bees finally won through, winning 2-0 with goals from Bob Booker and Chris Smith.
In the 2nd Qualifying Round, Barnet travelled to Isthmian League Division One side,Leytonstone & Ilford, a club that later evolved into the Redbridge half of current League Two side, Dagenham & Redbridge. Goals from Turner and Booker gave the Bees a 2-1 win and in the next round they won 1-0 away at Isthmian League Premier Division side, Hayes with Chris Hullett scoring the only goal.
In the 1st round proper, Barnet were drawn away to local rivals, Hendon, another Isthmian League club, and drew 1-1 with a goal from Steve Oliver. Barnet won the replay 1-0 at Underhill, Steve Robinson getting the goal for the Bees. In the 2nd round, Barnet beat APL side, Bangor City 4-1 with Steve Turner grabbing a hat trick, two of the goals coming from the penalty spot. Elwyn Roberts scored the other Barnet goal. However, Barnet's cup run came to an end in the 3rd round with a 2-1 defeat away at Nuneaton Borough, Steve Robinson getting the consolation goal for the Bees.
The following season saw the Bees go out again at the first attempt, losing 1-0 in the 3rd Qualifying Round at home to Harlow Town of the Isthmian League. 1981-82 was no better with the Bees going out at the same stage, this time away at Hendon, the Greens wining 2-1 with Barnet's goal coming from Colin Barnes.
1982-83 did, at least, see Barnet get through the first stage, winning 2-1 in the 3rd Qualifying Round at home to Metropolitan Police of the Isthmian League, Division One. Stewart Atkins and Colin Barnes got the Barnet goals. In the 1st Round proper, Barnet won 2-0 away at Woking, then a struggling Isthmian League Premier Division side, with goals from Peter Brown and Steve Ragan. However, in the 2nd round, Barnet went down 2-1 at home to Ilkeston Town in a match better known for the terrible behaviour of the visiting supporters. Colin Barnes scored the Barnet goal.
The next season, 1983-84, saw Barnet reach the 4th round of the FA Trophy. In the 3rd Qualifying Round, Barnet won 3-1 away at Isthmian League, Hayes with two goals from Steve Mahoney and one from Stewart Atkins. In the 1st Round proper, Barnet were drawn at home to again to Dartford, who were to end the season as Southern League Champions and win promotion to the Alliance Premier League. The Bees won 3-0 with goals from John Margerrison, John Docker and Nicky Evans.
In the 2nd round, Barnet beat Northern side, North Shields 4-1 with two goals apiece for Stewart Atkins and Nicky Evans. The Bees progressed through the 3rd Round with another home win, this time against Kidderminster, who had won promotion to the APL the previous season, Steve Ragan and Stewart Atkins scored the goals. However, the Bees went out at the 4th Round stage losing 1-0 away at Northwich Victoria in a close fought match.
In 1984-85, Barnet were drawn away at Dagenham in the 1st Round and drew 3-3. This was before the daggers had merged with Redbridge Forest and the Bees goals came from John Margerrison, Steve Mahoney and Steve Ragan. In the replay at Underhill, Barnet won 3-2 with goals from Eddie Stein, Steve Mahoney and Steve Ragan. In the 2nd round, Barnet won 1-0 away at Gretna courtesy of an Ian Ferguson penalty. Barnet went out in the 3rd round following a gruelling four match tie against Runcorn. After a goalless draw in the first match at Runcorn, the replay at Underhill ended in a 1-1 draw with Steve Mahoney scoring for Barnet. The 2nd replay was also at Underhill and ended goalless. Finally, in the 3rd replay, the tie was settled with Runcorn winning comprehensively 4-0 at Runcorn.
1985-86 saw Barnet lose 1-0 at home to Wycombe Wanderers, but the following season saw the Bees reach the 4th Round again. In the 1st Round they won 6-0 at home to Wokingham Town from the Isthmian League, Premier Division. Barnet's goals came from John Margerrison, Steve Mahoney, Gary Roberts and a hat trick for Nicky Evans.In the 2nd Round, the Bees were held 1-1 at home by another Isthmian League side, this time, Hitchin Town. Dave Sansom scored for the Bees. In the replay at Hitchin, Barnet won 5-0, with goals from Evans, Sansom (2) and Roberts (2). The 3rd round tie against Boston United went to three matches. The first match ended 1-1 at Underhill with Sansom scoring for Barnet. The replay at Boston ended 3-3 with Sansom scoring again and Andy Beattie scoring twice for the Bees. In the 2nd replay at Cambridge United's Abbey Stadium, Barnet won 3-0 with Sansom scoring twice and Eddie Stein scoring the other. Barnet then went out in the 4th round to a shock 1-0 home defeat at the hands of Southern League side, Fareham Town.
In 1987-88, Barnet were drawn against Isthmian League, Windsor & Eton in the 1st Round. The first match at Windsor ended in a 1-1 draw with Barnet's goal coming from Keith Alexander. In the replay at Underhill, Lee Payne and Dave Sansom scored in a 2-1 win for the Bees. In the 2nd round, were held to a goalless draw at home to Southern league, Bromsgrove who then knocked the Bees out of the tournament by winning the replay 3-1, Dave Sansom scoring the Bees goal. That was the last time that Barnet managed to win an FA Trophy match prior to winning the Conference title in 1991 and gaining promotion to the Football League, going out in the 1st Round in all three seasons.
In 1988-89, Barnet were held 1-1 by Southern League, Gravesend, Richard Nugent scoring for Barnet and the same player scored Barnet's goal in the replay. However, Gravesend won the match 2-1. The following season, 1989-90, Barnet lost 2-0 away at another Southern League side, this time, Weymouth and in the promotion season, 1990-91, Barnet were knocked out by Farnborough, who ended the season as Southern League champions and were promoted to the Conference just as Barnet were leaving it. Andy Clarke and Paul Richardson scored for Barnet but the bees lost 3-2 at Underhill. At the end of the season, Barnet won the GM Vauxhall Conference title and were promoted to the Football League Division Four.