application.yml

application:
  primary:
    config:
      foo: primaryfoo
      bar: primaryboo
  secondary:
    config:
      foo: secondaryfoo
      bar: secondaryboo

Config.java

@ConfigurationProperties("*.config")??
public class Config {
    private String foo;
    private String bar;

    public String getFoo() {
        return foo;
    }

    public void setFoo(String foo) {
        this.foo = foo;
    }

    public String getBar() {
        return bar;
    }

    public void setBar(String bar) {
        this.bar = bar;
    }
}