Even though he set out with the idea for the improvement of Uruguayan football, he never coached professionally in Uruguay. Markarian started his career in 1974 coaching the Reserves of Club Atlético Bella Vista of Uruguay and went on to coach the first team. Markarian made his professional coaching debut as a coach for the football club, Olimpia Asunción of Paraguay in 1983. He won the Paraguayan league with Olimpia the very same year he started coaching in 1983 and then again in 1985. After his four-year stay at Olimpia, he made the move to the Paraguayan club, Sol de America, leading them to win the Torneo Republica and to become the Paraguayan league runner-up in 1989. He then made the move to another Paraguayan giant, Cerro Porteño, winning the Torneo Republica in 1990.