Polls will open at 7:00 a.m. local time (12:00 GMT) and close at 5 p.m. President Guillermo Lasso has declined to run for a second four-year term.
Troops will ensure security at polling places under the state of emergency, which President Lasso announced last week following the killing of Fernando Villavicencio, a top presidential candidate from the conservative Construye Movement.
Villavicencio, an investigative journalist, was gunned down at a campaign rally on August 9. Ecuadorean media reported a shooting near the campaign venue of parliamentary contender Daniel Noboa just three days before the polls.
The Andean nation saw a spike in violence this year associated with drug cartels fighting for control of smuggling routes. The United Nations says it has been aware of attacks and threats against political candidates, other public figures and journalists.