In a multi-project build, you can use the gradle-jacocolog plugin to aggregate coverage information across subprojects. The plugin is really for logging the coverage data, but it can also perform aggregations.
Configure your Jacoco like you would normally, then apply the plugin to the root project:
plugins {
id 'org.barfuin.gradle.jacocolog' version '1.2.3'
}
After that, you can:
gradle jacocoAggregatedReport
to display the aggregated coverage. There is also a jacocoMergeSubprojects task which will just create a merge coverage file, if you want to process it in some other way.
Hope this helps!
(Full dislosure: I am the author of gradle-jacocolog.)