Speaking to UGO, Whithouse explained that the team behind the show had started to tell "bigger, even more kind of epic stories" in the second season.
However, he admitted that it was difficult to sustain the threat from Lucy (Lyndsey Marshal) and Kemp (Donald Sumpter) for a whole season.
"It was kind of difficult keeping the momentum up with them, so I think we realised when we went to the third series that it’s good to mix it up a bit," he said. "So we’ve done something slightly different in the third series in terms of who our villains or what our threat is."
Whithouse added that the third season will return to the more everyday stories of the early episodes.
"We wanted to keep the ambition and the epic nature of the series too but also put in more of the domesticity from the stories of the week of series one," he said. "So it was an opportunity to take the best of both bits of series one and series two and put them together."
The third season of Being Human is expected to begin in January.