If you have more than one main class, you need to explicitly configure the main class in each profile:
<profiles>
<profile>
<id>profile1</id>
<properties>
<spring.boot.mainclass>com.SomeClass</spring.boot.mainclass>
</properties>
</profile>
<profile>
<id>profile2</id>
<properties>
<spring.boot.mainclass>com.SomeOtherClass</spring.boot.mainclass>
</properties>
</profile>
</profiles>
…
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<version>1.5.2.RELEASE</version>
<executions>
<execution>
<goals>
<goal>repackage</goal>
</goals>
<configuration>
<mainClass>${spring.boot.mainclass}</mainClass>
</configuration>
</execution>
</executions>
...
</plugin>
See spring-boot:repackage