The Central Transportation Planning Staff (CTPS), the support staff to the Boston Region Metropolitan Planning Organization uses a traditional four step model to support various transportation planning projects, plans, and air quality conformity activities. Due to the multimodal nature of the Boston’s region’s transportation system; off-road transit modes such as commuter rail, ferry, and rapid transit services historically were calculated off-model and added to the emissions calculated from the on-road analysis. CTPS developed a methodology that integrates the emission rates generated from the on-road MOVES Model with off-road transit emissions in an automated approach. The off-road transit modes; such as commuter rail, ferry, and rapid transit represent a diverse set of vehicle types, technology, and fuel use. The commuter rail fleet is powered by several different locomotive types, the ferry service includes several different boat sizes, and the rapid transit includes duel modes vehicles along with third rail power consumption, which has created challenges in calculating emissions. The methodology integrated the travel demand modeling software Transcad with the entire air quality analysis for both on-road and off-road transportation modes. The method utilizes the latest guidance on emissions from EPA to streamline the calculations of volatile organic compound, nitrous oxides, carbon monoxides, and carbon dioxide for all transportation modes, allowing easily generating inventories and performing project level analysis. The integration of the travel demand model with on-road and off-road transit vehicle emissions has allowed CTPS to examine transportation projects in a more efficient manner, which other multimodal regions can benefit from.