This paper provides empirical evidence of changes in the productivities of manufacturing firms in Indonesia over time, in the form of total factor productivity (TFP), from 1990 to 2010 with and without considering carbon dioxide (CO 2 ) emissions. Employing cleaned and balanced panel datasets for four periods, the analysis enables an evaluation of the impact of implemented policies or economic circumstances during each period. The Malmquist productivity index is employed to estimate TFP without CO 2 emissions over time, whereas the Malmquist-Luenberger productivity index is applied to estimate TFP with CO 2 emissions over time. Furthermore, the influence of energy factors on environmental productivity is also investigated. The results show that on average, TFP with CO 2 emissions over time has grown faster than TFP without CO 2 emissions, particularly for periods 1, 2, and 4. Technical progress is the basis of productivity growth after removing energy subsidies, and the change in environmental productivity is associated with the adjusted energy prices. Constructive policy designs can be derived from this paper that will enhance manufacturing sector performance after changes in the prices of oil commodities.