We examine the time evolution of cold atoms (impurities) interacting with an environment consisting of a degenerate bosonic quantum gas. The impurity atoms differ from the environment atoms, being of a different species. This allows one to superimpose two independent trapping potentials, each being effective only on one atomic kind, while transparent to the other. When the environment is homogeneous and the impurities are confined in a potential consisting of a set of double wells, the system can be described in terms of an effective spin-boson model, where the occupation of the left or right well of each site represents the two (pseudo)-spin states. The irreversible dynamics of such system is here studied exactly, i.e. not in terms of a Markovian master equation. The dynamics of one and two impurities is remarkably different in respect of the standard decoherence of the spin-boson system. In particular, we show: (i) the appearance of coherence oscillations, (ii) the presence of super and subdecoherent states that differ from the standard ones of the spin-boson model, and (iii) the persistence of coherence in the system at long times. We show that this behaviour is due to the fact that the pseudospins have an internal spatial structure. We argue that collective decoherence also prompts information about the correlation length of the environment. In a one-dimensional (1D) configuration, one can change even more strongly the qualitative behaviour of the dephasing just by tuning the interaction of the bath.