The aims of this study were to calculate greenhouse gas (GHG) emissions and to identify the trends of GHG emission intensity, based on meat production from the livestock sector in Indonesia, which had not been done before. The total emissions from the livestock sector from 2000 to 2015 in Indonesia were calculated using the 2006 Intergovernmental Panel on Climate Change Guideline (2006 IPCC GL) using Tier 1 and Tier 2, with its default values and some of the country specific data that were found in the grey literature. During 2000 to 2015, the change from the Tier 1 to Tier 2 methods resulted in an approximately 7.39% emission decrease from enteric fermentation and a 4.24% increase from manure management, which resulted in a 4.98% decrease in the total emissions. The shared emission from manure management increased by about 9% and 6% using Tier 1 and Tier 2, respectively. In contrast with the total emissions, the overall emission intensity in Indonesia decreased (up to 60.77% for swine), showing that the livestock productivity in Indonesia has become more efficient. In order to meet the meat demand with less GHG emissions, chicken farming is one option to be developed. The increased emission and share from manure management indicated that manure management system needs to be of concern, especially for beef cattle and swine.