Updates on this : Got it to work, turns out as @Reguel said, the JDT compiler wont play with a javaagent. I got around this by using the offline mode of jacoco, and copying the generated classes from the classes directory in the correct target/classes and target/test-classes directories . This is what the pom section looks like : [Gist Of pom.xml parts][1] [1]: https://gist.githubusercontent.com/TareqK/3fbbd05c9a61116083872f9497a4e7a8/raw/528696c54214b546f5fc2541a83dfdf7b45a8d94/Jacoco%2520With%2520Axon%2520Ivy You also need to set the <testOutputDirectory> as well, otherwise it wont work The reports are generated in the target/site/jacoco folder, and the jacoco.exec file is in the target folder as well

Updates on this : Got it to work, turns out as @Reguel said, the JDT compiler wont play with a javaagent. I got around this by using the offline mode of jacoco, and copying the generated classes from the classes directory in the correct target/classes and target/test-classes directories . This is what the pom section looks like : [Gist Of pom.xml parts][1] [1]: https://gist.githubusercontent.com/TareqK/3fbbd05c9a61116083872f9497a4e7a8/raw/528696c54214b546f5fc2541a83dfdf7b45a8d94/Jacoco%2520With%2520Axon%2520Ivy The reports are generated in the target/site/jacoco folder, and the jacoco.exec file is in the target folder as well