When recombination in PN junction occurs, which atom becomes an ion? In an unbiased PN junction, when the carriers recombine to form a depletion layer , it is said that immobile ions are formed.
We know that the conduction band electrons in N type are not associated with any particular atom. So when the conduction band electron diffuses to the P type region, which atom becomes an ion?
 A: None, really. Such junctions form in semiconductor crystals. Those are remarkable materials. Let's look at electrons in solids first. 
Many atoms have weakly bound valence electrons in outer orbits. These orbits would have specific energies if the atom existed in isolation. But when man atoms are packed together and their outer orbits overlap, the energy of these orbits shift slightly. Electrons in those orbits now can have a band of possible energies.
Now those weakly bound electrons are good for carrying currents, but to hop through the material the overlapping orbits better not be completely filled. There wouldn't be room for the moving electron. In metals, there's in fact a band which is about half filled. Ideal - there's plenty of room for electrons to move, but also still enough electrons to move.
Semiconductors have a full and an empty band close together, and with some external help (doping, electric fields, etc) this can be used to switch from conducting to non-conducting.
Regardless, as the outer orbits overlap and join to form a band, the electrons in that band no longer belong to a single orbit and therefore a single atom. At the quantum level, the probability function of the electron is smeared out over the crystal. And thus it's not sensible to talk about the exact atoms ionized. 
A: Before the N type material is brought into contact with the P type material there will be an equilibrium between [N-type doping atoms with all electrons] and [Ionized N-type doping atoms]. So some atoms all across the bulk of the material will be ions, which ones will change over time. 
When the N-type material is brought into contact with a P-type material the equilibrium will shift. Near the junction most (all?) atoms will be ionzed since the region will be depleted of free electrons.
So the short answer the your question is: The atoms near the junction.
