The club was created in 1998 as a result of the merger between former Serie C2 (fourth division) teams Albinese Calcio and S.C. Leffe, respectively from Albino and Leffe, two neighboring towns. In their first season, the club finished 2nd in the Serie C2 and won a promotion after defeating Modena in the Girone A playoffs. After rising to the Italian Serie C1 (third division), they performed at the middle of the pack, finishing 9th in 2000 and 13th in 2001.
However, in 2002, the Seriani went to the finals of the Coppa Italia Serie C, where they defeated Livorno 2–1 at home before losing 2–3 on the road. They won the tournament on the tiebreaker (Most away goals scored).In league play they again finished 13th. In 2003, AlbinoLeffe, under coach Elio Gustinetti, finished second in league play before heading to the promotion play-off. There, they defeated Padua in the semifinals, then had a surprising triumph over Pisa Calcio final, which pushed them up to Serie B.
The team plays its home games at the Atleti Azzurri d'Italia stadium in Bergamo, the chief-town of the province where both Albino and Leffe are located, on account of the Leffe municipal stadium's low capacity (2,260 seats). AlbinoLeffe used to play there before its promotion to Serie B. Even though AlbinoLeffe was considered to be an outsider in Serie B, which historically includes several former Scudetto winners, the team remerkably managed to avoid relegation in the last two seasons. In 2005–2006, after a great comeback in the second half of the season following the appointment of Emiliano Mondonico as new head coach, Albinoleffe ended the season in eighteenth place and managed to save itself from relegation by prevailing in the playouts against Avellino (score: 2–0, 2–3). The 2006–2007 Serie B campaign, the fourth consecutive for the small Lombard team, ended with a good tenth place, well ahead of the relegation zone.
Historically, AlbinoLeffe's home games have been characterized by very low attendance, as shown by the average 2,400 spectators per game in the 2006–07 season, the most successful in the club history.
With local hero Gustinetti back in charge of the team and despite a lineup composed of relative unknowns, the club's 2007–08 campaign started surprisingly well, with the team leading the Serie B table for a few weeks and arousing the interest of the national media, which began providing regular coverage of the team's games. This has thus far failed to improve the club's low home attendance, however. During the season, AlbinoLeffe confirmed as a potential candidate for direct promotion to Serie A, however a string of poor results, ended with four consecutive home defeats, the final one being a 0–4 loss to Rimini, denied them the chance to achieve a place in the top two, and persuaded club chairman Gianfranco Andreoletti to sack Gustinetti, who then confirmed not to be in good relationships with the chairman, and appoint youth team coach Armando Madonna as caretaker boss for the final regular season match and the following promotion playoffs. Even after a 1–0 loss to Brescia, AlbinoLeffe managed to win at home in the second leg (2–1) and qualified for the final against Lecce. In the first leg they suffered a 1–0 loss. On 15 June the second match was played in Lecce and the result of the match was 1–1 so AlbinoLeffe didn't reach Serie A.