How can I add users to the inMemoryAuthentication builder after it has been built?

The following code will do what you are asking:

@Configuration
@EnableWebMvcSecurity
public class WebSecurityConfig extends WebSecurityConfigurerAdapter {

    @Override
    protected void configure(HttpSecurity http) throws Exception {
        //whatever here
    }

    @Override
    protected void configure(AuthenticationManagerBuilder auth) throws Exception {
        auth.userDetailsService(inMemoryUserDetailsManager());
    }

    @Bean
    public InMemoryUserDetailsManager inMemoryUserDetailsManager() {
        final Properties users = new Properties();
        users.put("user","pass,ROLE_USER,enabled"); //add whatever other user you need
        return new InMemoryUserDetailsManager(users);
    }

}

Using the InMemoryUserDetailsManager you configured above a super simple controller that just adds and checks for the existence of a user would look like:

@RestController
@RequestMapping("user")
public class SimpleSecurityController {

    private final InMemoryUserDetailsManager inMemoryUserDetailsManager;

    @Autowired
    public SimpleSecurityController(InMemoryUserDetailsManager inMemoryUserDetailsManager) {
       this.inMemoryUserDetailsManager = inMemoryUserDetailsManager;
    }

    @RequestMapping("exists/{username}")
    public boolean userExists(@PathVariable("username") String username ) {
        return inMemoryUserDetailsManager.userExists(username);
    }

    @RequestMapping("add/{username}/{password}")
    public String add(@PathVariable("username") String username, @PathVariable("password") String password) {
        inMemoryUserDetailsManager.createUser(new User(username, password, new ArrayList<GrantedAuthority>()));
        return "added";
    }
}

Also note that if you are using Spring Boot's autoconfiguration you will need to add

@EnableAutoConfiguration(exclude = SecurityAutoConfiguration.class)

to prevent Spring Boot from trying to autoconfigure security

Update As noted by @AdamMichalik, @EnableWebMvcSecurity is deprecated and should be replaced by @EnableWebSecurity

I changed this code:

inMemoryUserDetailsManager.createUser(new User(username, password, new ArrayList<GrantedAuthority>()));

from @geoend´s answer to:

inMemoryUserDetailsManager.createUser(User.withUsername(username).password(password).roles("USER").build());

because by default, a new user doesn't have any permissions.