The 58-year-old officially resigned from his post on Wednesday after just seven games in charge of Les Olympiens, who hired him to replace Igor Tudor over the summer.
Marcelino oversaw wholesale changes in the transfer market, with the likes of Dimitri Payet, Matteo Guendouzi and Alexis Sanchez moving on, while Pierre-Emerick Aubameyang, Iliman Ndiaye, Ismaila Sarr and Geoffrey Kondogbia were among those to arrive.
Despite navigating their first five Ligue 1 fixtures unbeaten, Marseille have experienced an indifferent start to the new term, only taking one point away from clashes with Nantes, Metz and most recently Toulouse.
The French giants also suffered a disheartening Champions League qualifying exit to Greek side Panathinaikos, and discontent among the Orange Velodrome faithful has hit new heights over the past few days.
Earlier this week, senior club figures and staff chaired meetings with Marseille supporter groups, and members of the club's ultras reportedly threatened Olympiens officials during the discussions.
The internal crisis led to Marcelino bidding a swift farewell, and the former Athletic Bilbao head coach took to social media to offer his view on the matter, claiming that the basic principles of respect had been "violated" by "serious threats, insults and slander".
"We believe that the minimum respect due to the people and professionals who manage the club has been violated here," L'Equipe quotes Marcelino as writing.
"Today's unstable situation clearly indicates that the sports project for which we were recruited cannot be carried out. We set out to achieve the desired objectives and, given our professional experience, were convinced of the team's rise, its progress was there.
"The desire for intimidation and the individual attacks of which the president and his steering committee were the target on Monday suggest an uncertain future during which the working conditions are not the most appropriate for exercise our profession with safety and with the normality usually inherent in a football club.
"The withdrawal of the president and his steering committee due to the serious threats, insults and slander they received, added to the climate of high tension which arrived in this two-month period, all this despite the professionalism and involvement of the technical staff make our retention at OM impossible."
Alongside Marcelino, club president Pablo Longoria was also said to have been the target of threats by the Olympiens ultras, who apparently accused him of making money unlawfully through the club's transfer business.
Longoria went as far as to hand over an audit containing all of his personal dealings to prove his innocence, but the 37-year-old's family were allegedly subjected to comments "based on causing fear".
Jacques Abardonado has been placed in interim charge ahead of Marseille's Europa League opener with Ajax on Thursday, which precedes Sunday's trip to Paris Saint-Germain in Le Classique.