Spanish Football Federation (RFEF) president Luis Rubiales announced Enrique's departure at a press conference, with assistant coach Robert Moreno set to replace him.
Moreno was on the bench against Malta and again against the Faroe Islands and Sweden earlier this month, but the Federation insisted that Luis Enrique was still coaching the team from a distance, choosing the squad, watching training sessions remotely and in constant contact with his staff.
"We will try to leave Luis Enrique's work at the top, get to the Euros and win it". "We will have a ideal memory of him", Rubiales told a news conference. He will remain in charge for the same duration of the contract that was already signed.
Moreno said: "I want to thank you [the RFEF] for placing your trust in us".
Moreno added: "It's a bittersweet day".
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He said: "Since I was 14 years old, I have thought about reaching the highest level, but I didn't expect it this way".
Since then, Luis Enrique had continued working remotely from his home in Barcelona, receiving video feeds of practices and talking to Moreno and his other assistants.
The former Barca tactician took charge of the 2010 World champions July 2018 following the nation's disappointing showing at last year's World Cup.
Spain announced Enrique's absence from the Euro 2020 qualifier with Malta back in March, citing "an urgent family matter".
RFEF sporting director Jose Francisco Molina said the decision to appoint Moreno was made in a bid to maintain continuity.
"A year ago we started a sports project that is going great and we wanted to continue that project".