The cast have told Newsbeat that there will be a "more serialised aspect" where stories carry throughout the run.
Fans will also get to delve deeper into the back stories of each of the four main characters.
And now that the time the programme will be aired has been revealed, they can afford to show more graphic violence.
"There's a lot of death in the show. When it's an eight o'clock show, it's like bish, bash, bosh, you know, somebody's dead. And now of course you see the blade go in and you see it come out the other side," says Tom Burke, who plays Athos.
"I think a lot of the darkness is there."
Howard Charles, who plays Porthos, backs what Tom says and thinks the later time slot is "a good thing".
"It's necessary for the story," he says.
"We needed to move the story on, move the characters on and dig deeper and find those new depths and I think that the time slot is one factor that enables us to do that.
"But of course it hasn't changed from last season, it's still a nine o'clock show. It's just when we shot season one, we shot it with the view to making it an eight o'clock show.
"Whereas this season we knew it was going to be nine o'clock, so you know there are sort of CGI elements, and things like that and a bit more blood, guts. But also psychologically, it is darker and therefore fuller."
The cast also says that they were very happy with the success of the first series.
Luke Pasqualino who plays D'Artagnan says it's a good reward for their hard work.
"It's always very flattering when you put your heart and soul into something for so long, like seven months, and then you're always kind of nervous to see how the audience will react to it.
"We've all had that extra push to make it even bigger and better than the first. It's been good. We're happy."
The Musketeers starts on BBC One on 2 January at 21:00 GMT.
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The new series of the BBC One hit show The Musketeers is returning with a "darker tone".