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Upcoming Large-Scale Structure surveys will likely become the next leading sources of cosmological information, making it crucial to have a precise understanding of the influence of baryons on cosmological observables. The Effective Field Theory of Large-Scale Structure (EFTofLSS) provides a consistent way to predict the clustering of dark matter and baryons on large scales, where their leading corrections in perturbation theory are given by a simple and calculable functional form even after the onset of baryonic processes. In this paper, we extend the two-fluid-like system up to two-loop order in perturbation theory. Along the way, we show that a new linear counterterm proportional to the relative velocity of the fluids could generically be present, but we show that its effects are expected to be small in our universe. Regardless, we show how to consistently perform perturbation theory in the presence of this new term. We find that the EFTofLSS at two-loop order can accurately account for the details of baryonic processes on large scales. We compare our results to a hydrodynamical $N$-body simulation at many redshifts and find that the counterterms associated with the leading corrections to dark matter and baryons start to differ between redshifts $z \approx 3$ and $z \approx 2$, signaling the onset of star-formation physics. We then use these fits to compute the lensing power spectrum, show that the understanding of baryonic processes will be important for analyzing CMB-S4 data, and show that the two-loop EFTofLSS accurately captures these effects for $\ell \lesssim 2000$. Our results are also potentially of interest for current and future weak lensing surveys.