In one aspect, a system for managing agricultural operations based on geo-referenced agricultural maps includes an agricultural machine and a computing system configured to: access a geospatial carbon intensity (CI) map associated with CI scores for a plurality of locations within a field, the geospatial CI map being based at least in part on input data associated with the field and/or one or more previous agricultural operations performed within the field; access data associated with a CI score threshold for each respective location of the plurality of locations within the field; and actively control an operation of the agricultural machine during the performance of an agricultural operation within the field so that the CI score for each respective location of the plurality of locations is maintained below the CI score threshold for the respective location.