Nonlinear optical (NLO) materials are becoming increasingly popular due to their wide range of applications in sub-bandgap photoelectric detection, photonic diodes, Q-switched/mode-locked pulse laser production, optical limiting, and optical switching. In this study, bare and doped (Co, Cu) alpha manganese dioxide (α-MnO2)/poly (methyl methacrylate) (PMMA) nanocomposite films were fabricated to investigate the effect of the in-gap states modulation triggered nonlinear absorption (NA) mechanisms on optical limiting. The structural characterization of bare and doped powders proved the successful incorporation of dopant metals into the α-MnO2 lattice. Linear absorption measurements revealed that the nanocomposite films have two distinct bands at around 230 nm and above 400 nm attributed to PMMA and bare, Co and Cu doped α-MnO2 nanoparticles, respectively. While the localized defect states of PMMA decreased with the addition of the nanoparticles, the localized defect states of the α-MnO2 increased with Co and Cu dopants. To reveal the NA behaviors and mechanisms of the nanocomposite films, open aperture Z-scan experiments were performed at 532 nm with 4 ns pulsed laser at various input intensities. The saturable absorption effect on the NA behavior of the nanocomposite films was observed with increasing input intensity due to the filling of the defect states of the nanoparticles by one photon absorption (OPA). Considering the bandgap energies and localized defect states of the nanocomposite films, it was revealed that the PMMA/MnO2 and PMMA/MnO2:Co nanocomposite films had the same NA mechanisms which are OPA, sequential two photon absorption, free carrier absorption and excited state absorption (ESA). Among these NA mechanisms, the ESA between the conduction band of MnO2:Cu nanoparticles and localized defect states of PMMA did not occur due to inconvenient energy differences between these states in PMMA/MnO2:Cu nanocomposite film. Therefore, this nanocomposite film had weaker NA behavior than other nanocomposite films. On the other hand, the larger number of localized defect states of the PMMA/MnO2:Co nanocomposite as compared to PMMA/MnO2 film caused stronger NA behavior. The PMMA/MnO2:Co nanocomposite film had stronger optical limiting feature than other nanocomposite films. In light of all results, these materials are potentially useful for constructing saturable absorbers and optical limiters by modulating in-gap states.