We present an analysis of Giant Molecular Clouds (GMCs) within hydrodynamic simulations of isolated, low-mass (M * ∼ 10 9 M ) disc galaxies. We study the evolution of molecular abundances and the implications for CO emission and the X CO conversion factor in individual clouds. We define clouds either as regions above a density threshold n H, min = 10 cm −3 , or using an observationally motivated CO intensity threshold of 0.25 K km s −1 . Our simulations include a non-equilibrium chemical model with 157 species, including 20 molecules. We also investigate the effects of resolution and pressure floors (i.e. Jeans limiters). We find cloud lifetimes up to ≈ 40 Myr, with a median of 13 Myr, in agreement with observations. At one tenth solar metallicity, young clouds ( 10 − 15 Myr) are underabundant in H 2 and CO compared to chemical equilibrium, by factors of ≈ 3 and 1 − 2 orders of magnitude, respectively. At solar metallicity, GMCs reach chemical equilibrium faster (within ≈ 1 Myr). We also compute CO emission from individual clouds. The mean CO intensity, I CO , is strongly suppressed at low dust extinction, A v , and possibly saturates towards high A v , in agreement with observations. The I CO −A v relation shifts towards higher A v for higher metallicities and, to a lesser extent, for stronger UV radiation. At one tenth solar metallicity, CO emission is weaker in young clouds ( 10−15 Myr), consistent with the underabundance of CO. Consequently, X CO decreases by an order of magnitude from 0 to 15 Myr, albeit with a large scatter.