After his retirement, Leis returned to Compostela as a coach. He took over as first team manager in March 1998 after the departure of Fernando Vázquez,[2] with the club in the La Liga relegation play-off places.[3] Leis guided them to victory in five of their remaining 11 matches,[4] but they still finished the season in 17th,[3] and faced a relegation play-off against Villarreal. A 0–0 draw at El Madrigal was followed by a 1–1 draw at home at San Lázaro, meaning Compostela lost on away goals and were relegated to the Segunda División after four years in the top flight.[2]
Leis was replaced by Antonio Maceda ahead of the new season, but Macedo lasted just nine games before departing in October with Compostela 13th in the Segunda División table.[5][6] After Pichi Lucas acted as interim manager for three games,[5] Leis returned as manager in late November. He was in charge for 15 matches, winning six,[7] but despite improving the club's league position to 8th[6] he left his position in March 1999.[7] Compostela would total five managers that season, with Zoran Marić and Andoni Goikoetxea both taking the reins after Leis's departure.[5]
For the 2003–04 season Compostela, who had by now slipped into Segunda División B, appointed Pichi Lucas as their permanent manager, but he departed in January with the club second from bottom.[8][9] After one match with Franck Passi in interim charge, Leis took over for his third spell as manager.[8] Compostela won just five of their remaining 18 matches, and were relegated to the Tercera División in 19th place.[9] Financial problems, which had meant players refused to play one of their matches against Conquense due to unpaid wages, also led to Compostela being demoted another step to Regional Preferente de Galicia, and Leis left the club.
Leis returned to management in January 2008, taking over at San Isidro in Segunda División B. He won only one of his 10 matches in charge, and lost eight, before departing in March[10] with the club bottom of the table. The rest of the season was no better, and they were relegated in last place.[11]