There are two different ways to feed SonarQube with information on unit tests execution and code coverage:

Project samples covering the different cases below are available on github that can be browsed or downloadedprojects/languages/java/code-coverage

See Component Viewer on Unit Test File or Quality Flows > Lack of Unit Tests to browse the results in the web interface.
See also the Manage Code Coverage by Unit Tests with Sonar blog post.

Reusing Existing Reports

Every analyzer supports the reuse reports mode.

To be reused by SonarQube:

First, tell SonarQube to reuse existing reports:

With Maven in your pom.xml file:

<sonar.dynamicAnalysis>reuseReports</sonar.dynamicAnalysis>

With Ant in your build.xml file:

<property name="sonar.dynamicAnalysis" value="reuseReports" />

With SonarQube Runner in your sonar-project.properties file:

sonar.dynamicAnalysis=reuseReports

Test Execution Reports

Tell SonarQube where your unit tests execution reports are: absolute or relative path to the directory containing your reports

With Maven in your pom file:

<sonar.junit.reportsPath>[baseDir]/myReports/myExecutionReports</sonar.junit.reportsPath>

With Ant in your build file:

<property name="sonar.junit.reportsPath" value="[baseDir]/myReports/myExecutionReports" />

With SonarQube Runner in your sonar-project.properties file:

sonar.junit.reportsPath=[baseDir]/myReports/myExecutionReports

Code Coverage Report 

First, tell SonarQube which code coverage engine has been used to generate the reports: jacoco, cobertura or clover.

<sonar.java.coveragePlugin>jacoco | cobertura | clover</sonar.java.coveragePlugin>

Then, tell SonarQube where to get the code coverage reports.

With Maven in your pom file:

<sonar.jacoco.reportPath>[baseDir]/myReports/myCodeCoverageReport</sonar.jacoco.reportPath>

With Ant in your build file:

<property name="sonar.jacoco.reportPath" value="[baseDir]/myReports/myCodeCoverageReport" />

With SonarQube Runner in your sonar-project.properties file:

sonar.jacoco.reportPath=[baseDir]/myReports/myCodeCoverageReport

Depending on the code coverage tool you used to generate your report, replace jacoco by cobertura or clover in the property name.

Using SonarQube Embedded Engine

Maven supports this mode with the following code coverage tools: JaCoCo, Cobertura and Clover.

The SonarQube Ant Task and the SonarQube Runner do not support this mode.

Before running an analysis with JaCoCo, the source code has to be compiled.

First, tell SonarQube to execute the unit tests and the code coverage tool:

Add this to your pom file:

<sonar.dynamicAnalysis>true</sonar.dynamicAnalysis>

Maven Project

With Maven, then, you just have to tell SonarQube which code coverage engine you wish to use: jacoco or cobertura or clover.

<sonar.java.coveragePlugin>jacoco | cobertura | clover</sonar.java.coveragePlugin>

Note that this property can be set at the SonarQube instance level through the web interface: Settings > Configuration > General Settings > Java.

Sample projects are available on github that can be browsed or downloaded:

Maven Multi-module Project and JaCoCo

For multi-module Maven projects, compute overall code coverage by unit tests across modules. This case clearly lies between unit tests and integration tests but this is widely used.

Sample projects are available on github that can be browsed or downloadedprojects/code-coverage/combined ut-it/maven/combined-ut-it-multimodule-maven-jacoco

Note that this project structure is not compatible with the below feature: mapping of unit tests and covered code.

 

Mapping of Unit Tests and Covered Code

The objective is to answer the following questions:

See Component Viewer on Unit Test File for more details.

A sample project is available on github that can be browsed or downloadedprojects/code-coverage/ut/maven/ut-maven-jacoco-runTests. What you need to add to your pom.xml to get this behavior is contained between "BEGIN/END: Specific to mapping unit tests and covered code" tags in the pom file. Note that you have to run the analysis with the coverage-per-test profile. Read the README file for more information.

Requires:

This feature is only available while using JaCoCo as the code coverage tool.

FAQ

0% code coverage reported, but unit tests are correctly executed

This problem occurs while using the Maven Cobertura Plugin and a special configuration of the Maven Surefire Plugin prevents the unit tests from being forked. This problem can be solved by removing the line "<forkMode>never</forkMode>" in the Maven configuration file (see SONAR-1445 and MCOBERTURA-70).

java.lang.Error: Unable to access JaCoCo Agent - make sure that you use JaCoCo and version not lower than 0.6.2

There can be several reasons for this error:
...
<plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-surefire-plugin</artifactId>
  <version>2.4.2</version>
  <configuration>
    <forkMode>never</forkMode> <!-- Do not set forkMode to never -->
    <reportFormat>xml</reportFormat>
    <testFailureIgnore>true</testFailureIgnore>
  </configuration>
</plugin>
...