Context. Feedback in the form of mass outflows driven by star formation or active galactic nuclei is a key component of galaxy evolution. The luminous infrared galaxy Zw 049.057 harbours a compact obscured nucleus with a possible far-infrared signature of outflowing molecular gas. Due to the high optical depths at far-infrared wavelengths, however, the interpretation of the outflow signature is uncertain. At millimeter and radio wavelengths, the radiation is better able to penetrate the large columns of gas and dust responsible for the obscuration. Aims. We aim to investigate the molecular gas distribution and kinematics in the nucleus of Zw 049.057 in order to confirm and locate the molecular outflow, with the ultimate goal to understand how the nuclear activity affects the host galaxy. Methods. We used high angular resolution observations from the Submillimeter Array (SMA), the Atacama Large Millimeter/submillimeter Array (ALMA), and the Karl G. Jansky Very Large Array (VLA) to image the CO J = 2–1 and J = 6–5 emission, the 690 GHz continuum, the radio centimeter continuum, and absorptions by rotationally excited OH. Results. The CO line profiles exhibit wings extending ~ 300 km s^-1 beyond the systemic velocity. At centimeter wavelengths, we find a compact (~ 40 pc) continuum component in the nucleus, with weaker emission extending several 100 pc approximately along the major and minor axes of the galaxy. In the OH absorption lines toward the compact continuum, wings extending to a similar velocity as for the CO are only seen on the blue side of the profile. The weak centimeter continuum emission along the minor axis is aligned with a highly collimated, jet-like dust feature previously seen in near-infrared images of the galaxy. Comparison of the apparent optical depths in the OH lines indicate that the excitation conditions in Zw 049.057 differ from those within other OH megamaser galaxies. Conclusions. We interpret the wings in the spectral lines as signatures of a nuclear molecular outflow. A relation between this outflow and the minor axis radio feature is possible, although further studies are required to investigate this possible association and understand the connection between the outflow and the nuclear activity. Finally, we suggest that the differing OH excitation conditions are further evidence that Zw 049.057 is in a transition phase between megamaser and kilomaser activity.