After guiding Benfica to second place, Graeme Souness remained in charge for a first full season. The Scottish brought in a handful of British players to the team, but only Michael Thomas, Mark Pembridge and Dean Saunders got regular playing time. To offset, Benfica lost the likes of Edgar Pacheco, Brian Deane and Scott Minto.

The season started with the qualifying rounds of the UEFA Champions League, which the club successfully passes, although not without drama. Domestically, Benfica fared better, quickly reaching the top spots by early October. However, a home draw with Alverca, starts a six-match win–less spree that put them in fifth place in the league and negatively impacted their Champions League campaign.

Benfica eventually regained their step in the Primeira Divisão. From late November till early February, they won 8 out of 9 matches, including seven in a row. This allowed them to battle the second place with Boavista with a match between in 14 March assuming significant importance. Benfica lost and started another downward spiral of erratic results that eventually led to the dismissal of Souness. Long-time assistant Shéu finished the season, with Benfica reaching 65 points, 14 less than Porto. Nuno Gomes had its best season of his career, scoring 34 goals in all competitions.

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