A four-goal second half inspired the resounding victory at the Estadio Federativo Reina del Cisne, with Danilo Carando's brace setting the tone in the midweek fixture.
Argentine attacker Carando broke the deadlock on the hour-mark before doubling LDU Loja's lead 12 minutes later.
Jonny Uchuari scored his second goal in less than a week as the home side took a three-goal lead with five minutes remaining.
LDU Loja heaped further misery on winless Deportivo Quito when Armando Gomez struck in the 90th minute.
After drawing their opening game last week, LDU Loja (+4) are now top of the standings with four points and a superior goal difference.
Emelec (+3) - winners of the first phase - have also collected four points from two rounds after easily accounting for Deportivo Cuenca 3-0.
Jose Quinonez, Angel Mena and Miller Bolanos were all on target as Emelec emerged triumphant at the Estadio George Capwell.
Mushuc Runa (+2), Independiente del Valle (+1) and LDU Quito (+1) are also level on points at the summit.
Wellington Sanchez and Fernando Lopez led Mushuc Runa to a 2-0 victory over Barcelona.
Independiente del Valle salvaged a 1-1 draw at home to Olmedo thanks to Armando Solis' 90th-minute equaliser.
Two goals in the final 15 minutes from Holger Matamoros and Juan Anangono helped LDU Quito to a 2-1 win against Universidad Catolica.
Meanwhile, Marwin Pita and Tito Valencia both scored in the space of two minutes as El Nacional downed cellar-dwellers Manta 2-1.
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