Caruana Galizia, 53, was one of Malta's most prominent public figures, thanks to a widely read blog she used to expose crime and corruption on the small but economically booming nation.
Her death -- her vehicle was reduced to a shell of twisted, burned metal in the fatal blast -- led to an outpouring of grief on Malta and an international outcry.
The three men charged with her murder -- brothers George and Alfred Degiorgio, aged 55 and 53 respectively, and Vincent Muscat, 55 -- pleaded not guilty in court in Valletta.
They were charged with manufacturing the bomb, with killing the journalist, with taking part in organised crime, as well as possession of explosives.
All three are Maltese and they sat motionless in the dock with their heads lowered before Magistrate Neville Camilleri. They will be kept in jail.
The three suspects were among 10 people arrested in an operation on Monday. The other seven have been released on police bail pending a probe of other evidence.
Much of Caruana Galizia's recent work had been centred on what the huge Panama Papers data leak revealed about corruption at the highest levels in Malta.
'There are crooks everywhere'
Her most explosive reports included allegations that members of Prime Minister Joseph Muscat's inner circle benefited from kickbacks on business deals and a controversial passports-for-investment scheme.
But she also focused on alleged dubious behaviour by prominent opposition and business figures, fuelling speculation she could have been the victim of mobsters.
During Monday's announcement of the arrests, Muscat said a joint team of police, military and security services swooped following a nearly seven-week investigation carried out with help from the FBI, Europol and Finnish intelligence.
Muscat's Labour Party government had offered a one million euro ($1.2 million) reward for information leading to a conviction of Caruana Galizia's killers.
But her sons denounced the reward as a publicity stunt and called on Muscat to resign over the state's failure to protect their mother and his attempts to silence her through legal suits when she was alive.
In her final post on Running Commentary, the blog she had written since 2008, Caruana Galizia voiced despair over the cronyism and sleaze she saw engulfing Malta.
"There are crooks everywhere you look now. The situation is desperate," she posted minutes before the fatal blast.
Since her death, an Italian prosecutor investigating suspected mafia fuel smuggling from Libya to Italy via Malta has suggested the murder could be linked to his case, which Caruana Galizia had written about.
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