Boltzmann codes are essential tools for studying cosmology. Most of the codes are based on a seminal work by Ma and Bertschinger. We found that the formalism employed in those codes has at least three possible problems which need to be understood. i) The equation of motion for baryons are gauge incompatible, ii) they break the Bianchi identity, and iii) it is not clear from the equations of motion which physical system is considered. In this work we revisit the baryon physics and address all the above mentioned issues, based solely on conservation of stress-energy tensor, resulting in taking into account a correction that is usually neglected and that is numerically small. We also study the tight coupling approximation up to the second order without choosing any gauge. We implement the improved baryon equations in a Boltzmann code and investigate the change in the estimate of cosmological parameters by performing an MCMC analysis. While in this paper we study the Lambda-CDM model only, our baryon equations can be easily implemented in other models and various modified gravity theories.