As I've answered here: You can put all the reports together in one folder (don't forget to call the different!) and use the merge mojo for that, or use a central unique file to all your reports by adding the flag "append":
-javaagent:append=true,destFile=/home/YourProject/report.exec
[Here][2] you'll find more information about how to configure the agent.
Hope it helps!
(this is a copy of my other answer to the same problem)
EDIT:
As long as you were asking for different kind of execution (unit and integration) I assume you are using different plugins for the execution of your tests.
What you have to do is to prepare two JaCoCo agents and give the argLine of them to the plugin that will run your test:
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.7.201606060606</version>
<executions>
<!--
Prepares the property pointing to the JaCoCo runtime agent which
is passed as VM argument when Maven the Surefire plugin is executed.
-->
<execution>
<id>pre-unit-test</id>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<destFile>${project.build.directory}/jacoco.exec</destFile>
<!--
Sets the name of the property containing the settings
for JaCoCo runtime agent.
-->
<propertyName>surefireArgLine</propertyName>
</configuration>
</execution>
<!--
Ensures that the code coverage report for unit tests is created after
unit tests have been run.
-->
<execution>
<id>post-unit-test</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<dataFile>${project.build.directory}/jacoco.exec</dataFile>
<!-- Sets the output directory for the code coverage report. -->
<outputDirectory>${project.reporting.outputDirectory}</outputDirectory>
</configuration>
</execution>
<!-- The Executions required by unit tests are omitted. -->
<!--
Prepares the property pointing to the JaCoCo runtime agent which
is passed as VM argument when Maven the Failsafe plugin is executed.
-->
<execution>
<id>pre-integration-test</id>
<phase>pre-integration-test</phase>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<destFile>${project.build.directory}/jacoco-it.exec</destFile>
<!--
Sets the name of the property containing the settings
for JaCoCo runtime agent.
-->
<propertyName>failsafeArgLine</propertyName>
</configuration>
</execution>
<!--
Ensures that the code coverage report for integration tests after
integration tests have been run.
-->
<execution>
<id>post-integration-test</id>
<phase>post-integration-test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<dataFile>${project.build.directory}/jacoco-it.exec</dataFile>
<!-- Sets the output directory for the code coverage report. -->
<outputDirectory>${project.reporting.outputDirectory}</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
Then you have to configure your plugins (normally used failsafe and surefire) for accepting the argLine created for the JaCoCo agents:
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${surefireArgLine}</argLine>
</configuration>
</plugin>
The same for the failsafe plugin.
