A complete microstructural characterization and phase transformation analysis has been performed for several Nb and Nb-Mo microalloyed low-carbon steels using electron backscattered diffraction (EBSD) and dilatometry tests. Compression thermomechanical schedules were designed resulting in the undeformed and deformed austenite structures before final transformation. The effects of microalloying additions and accumulated deformation were analyzed after CCT diagram development and microstructural quantification. The resulting microstructures ranged from polygonal ferrite and pearlite at slow cooling ranges, to a combination of quasipolygonal ferrite and granular ferrite for intermediate cooling rates, and finally, to bainitic ferrite with martensite for fast cooling rates. The addition of Mo promotes a shift in the CCT diagrams to lower transformation start temperatures. When the amount of Nb is increased, CCT diagrams show little variations for transformations from the undeformed austenite and higher initial transformation temperatures in the transformations from the deformed austenite. This different behavior is due to the effect of niobium on strain accumulation in austenite and its subsequent acceleration of transformation kinetics. This article shows the complex interactions between chemical composition, deformation, and the phases formed, as well as their effect on microstructural unit sizes and homogeneity.