The spin transition in LaCoO$_3$ has been investigated within the density-functional theory + dynamical mean-field theory formalism using continuous time quantum Monte Carlo. Calculations on the experimental rhombohedral atomic structure with two Co sites per unit cell show that an independent treatment of the Co atoms results in a ground state with strong charge fluctuations induced by electronic correlations. Each atom shows a contribution from either a $d^5$ or a $d^7$ state in addition to the main $d^6$ state. These states play a relevant role in the spin transition which can be understood as a low spin-high spin (LS-HS) transition with significant contributions ($sim$ $10$ %) to the LS and HS states of $d^5$ and $d^7$ states respectively. A thermodynamic analysis reveals a significant kinetic energy gain through introduction of charge fluctuations, which in addition to the potential energy reduction lowers the total energy of the system.
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