My childs dad walked out when I was pregnant and said he wasn’t ready to be a father. Not long after, I got with my now boyfriend and we have 2 kids of our own together, my other child calls my boyfriend daddy and has gone since he was old enough too as he was going to bring him up as his own. My child is now 3, his biological dad got in contact last year to say he had sorted his life out and wanted to be part of his life, I agreed they could get to know each other and build some contact up, it’s been nearly a year since they’ve been in touch with each other but my child doesn’t know it’s his real dad as he’s been calling my boyfriend daddy for so long, how do I explain to him who his real dad is?
First of all, his real dad is the one who's been caring for him for the last three years; it has nothing to do with biology.
In terms of his biological father, I don't think with a three-year-old you need to go into a lot of detail that he probably won't understand anyway.
You can just say something like, "[Bio dad] was your first daddy, but he had to go away and couldn't take care of you, so [Step dad] became your daddy. Now [Bio dad] is back, so you have two daddies."
Once he's old enough to understand how babies are made, you can explain that [Bio dad] is his biological father.
The first step is that you figure out what exactly you want to communicate to your son, and what you want to achieve with that communication. This probably should involve talking with both your boyfriend and your ex. "Real dad" is a complicated and problematic concept, and I'd shy away from it.
A set of goals that seems reasonable to me would be: a) Be honest with your son. b) Continue the good relationship between your son and your boyfriend c) Deepen the relationship between your son and your ex
Your boyfriend has become "Daddy" for your son, and there is no dishonesty in this. Once your son asks enough about his origins the moment comes to tell him that your ex rather than your boyfriend sired him. Don't make a big deal out of it, as he will likely follow your lead on how to react to such information.
If you and your ex want him to also take on more of a father-role, explore potential appelations for him. Maybe he could become "Dad FirstName"? "Papa"? Basically, the goal is avoid giving your son the impression that he is losing the father he has known all his life, and instead have him gain a second one.
I would avoid the "he had to go away"-phrasing GentlePurpleRain proposes. "Sometimes Dads go away" is true, but it is also frightening. If you can keep this concept out of the changes to your son's life, it might be better.