Raman, photoluminescence, and transport properties of nitrogen-doped ultrananocrystal diamond (UNCD) films were investigated following treatment with low energy microwave plasma at room temperature. The conductivity of nitrogen-doped UNCD films treated by microwave plasma was found to decrease slightly due to the reduced grain boundaries. We speculate that the plasma generated vacancies in UNCD films and provided heat for further mobilizing the vacancies to combine with the impurities, which led to the formation of the silicon-vacancy (Si-V) and nitrogen-vacancy (N-V) defect centers. The generated color centers were found to be distributed uniformly in the samples using a PL mapping technique. The PL emitted by the plasma treated nitrogen-doped UNCD film was strongly enhanced in comparison with the untreated films.