How to customise the Jackson JSON mapper implicitly used by Spring Boot?

A lot of things can configured in applicationproperties. Unfortunately this feature only in Version 1.3, but you can add in a Config-Class

@Autowired(required = true)
public void configureJackson(ObjectMapper jackson2ObjectMapper) {
    jackson2ObjectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
}

[UPDATE: You must work on the ObjectMapper because the build()-method is called before the config is runs.]

The documentation states several ways to do this.

If you want to replace the default ObjectMapper completely, define a @Bean of that type and mark it as @Primary.

Defining a @Bean of type Jackson2ObjectMapperBuilder will allow you to customize both default ObjectMapper and XmlMapper (used in MappingJackson2HttpMessageConverter and MappingJackson2XmlHttpMessageConverter respectively).

You can configure property inclusion, and numerous other settings, via application.properties:

spring.jackson.default-property-inclusion=non_null

There's a table in the documentation that lists all of the properties that can be used.

If you want more control, you can also customize Spring Boot's configuration programatically using a Jackson2ObjectMapperBuilderCustomizer bean, as described in the documentation:

The context’s Jackson2ObjectMapperBuilder can be customized by one or more Jackson2ObjectMapperBuilderCustomizer beans. Such customizer beans can be ordered (Boot’s own customizer has an order of 0), letting additional customization be applied both before and after Boot’s customization.

Lastly, if you don't want any of Boot's configuration and want to take complete control over how the ObjectMapper is configured, declare your own Jackson2ObjectMapperBuilder bean:

@Bean
Jackson2ObjectMapperBuilder objectMapperBuilder() {
    Jackson2ObjectMapperBuilder builder = new Jackson2ObjectMapperBuilder();
    // Configure the builder to suit your needs
    return builder;
}

I am answering bit late to this question, but someone, in future, might find this useful. The below approach, besides lots of other approaches, works best, and I personally think would better suit a web application.

@Configuration
@EnableWebMvc
public class WebConfiguration extends WebMvcConfigurerAdapter {

 ... other configurations

@Override
    public void configureMessageConverters(List<HttpMessageConverter<?>> converters) {
        Jackson2ObjectMapperBuilder builder = new Jackson2ObjectMapperBuilder();
        builder.serializationInclusion(JsonInclude.Include.NON_NULL);
        builder.propertyNamingStrategy(PropertyNamingStrategy.CAMEL_CASE_TO_LOWER_CASE_WITH_UNDERSCORES);
        builder.serializationInclusion(Include.NON_EMPTY);
        builder.indentOutput(true).dateFormat(new SimpleDateFormat("yyyy-MM-dd"));
        converters.add(new MappingJackson2HttpMessageConverter(builder.build()));
        converters.add(new MappingJackson2XmlHttpMessageConverter(builder.createXmlMapper(true).build()));
    }
}