On 24 July 2014, Eliseu signed for Portuguese champions S.L. Benfica for an undisclosed fee rumoured to be around €1.5 million, on a two-year deal with the option for a further one.
He was reunited at the club with former Belenenses coach Jorge Jesus, who had previously tried to acquire his services.

Eliseu made his official debut on 10 August 2014, playing the full 120 minutes as a left back in a penalty shootout win against Rio Ave for the Supertaça Cândido de Oliveira (0–0 draw).
He scored his first goal for his new team with a strike from outside the box, which ended up being the winning goal at Boavista FC's artificial turf.
His second came on 21 September also in the league, striking from 30 meters out in a 3–1 home success over Moreirense.

On 21 February 2015, Eliseu also netted from long range against Moreirense in the league (3–1 away win).
He ended the campaign with 33 games across all competitions, as Benfica won the national championship for the second time in a row.

It was reported by Portuguese press in December 2017 that Eliseu had been told by manager Rui Vitória that he would be released at the turn of the year.
This did not happen, but in March it was confirmed that his contract would not be renewed once it expired at the end of the season.
In May 2019 he returned to the Estádio da Luz to celebrate the team's league win by driving around the pitch on his scooter, wearing sunglasses at night; he had marked the victory two years prior in the same way.
On 24 July 2014, Eliseu signed for Portuguese champions S.L. Benfica for an undisclosed fee rumoured to be around €1.5 million, on a two-year deal with the option for a further one. He was reunited at the club with former Belenenses coach Jorge Jesus, who had previously tried to acquire his services.
Eliseu made his official debut on 10 August 2014, playing the full 120 minutes as a left back in a penalty shootout win against Rio Ave for the Supertaça Cândido de Oliveira (0–0 draw). He scored his first goal for his new team with a strike from outside the box, which ended up being the winning goal at Boavista FC's artificial turf. His second came on 21 September also in the league, striking from 30 meters out in a 3–1 home success over Moreirense.
On 21 February 2015, Eliseu also netted from long range against Moreirense in the league (3–1 away win). He ended the campaign with 33 games across all competitions, as Benfica won the national championship for the second time in a row.
It was reported by Portuguese press in December 2017 that Eliseu had been told by manager Rui Vitória that he would be released at the turn of the year. This did not happen, but in March it was confirmed that his contract would not be renewed once it expired at the end of the season. In May 2019 he returned to the Estádio da Luz to celebrate the team's league win by driving around the pitch on his scooter, wearing sunglasses at night; he had marked the victory two years prior in the same way.
Eliseu