After a scoreless first half, Arroyo produced the decisive moment of the match at Loja's Estadio Federativo Reina del Cisne in the 71st minute, curling a free-kick over the wall and into the top corner.
LDU Loja moved to 11 points from five matches, while Emelec (10 points), who have only played four games, sit second after a 2-1 over Universidad Catolica.
Denis Stracqualursi and Luis Miguel Escalada struck in the space of eight minutes for Emelec and despite Enzo Cuesta's second-half goal for Catolica, the reigning champions held on for victory.
Loja and Emelec are the only two teams in Ecuador's top tier without a loss so far this season, while Olmedo dropped off that list after a 1-0 loss to Independiente del Valle on Friday.
Olmedo sit third on eight points, ahead of Independiente and Manta on goal difference.
Manta defeated Deportivo Cuenca, while El Nacional trumped Barcelona 1-0 and LDU Quito were held to a scoreless draw by Mushuc Runa.
