I was able to know whats going on, I am using custom reader/processor/writer. When springboot application starts it actually try to do dependency injection of this custom beans beans where I have written some application logic.

Example

** TestConfiguration.class**

    @Configuration
    @EnableBatchProcessing
    public class TestConfiguration {

        @Bean
        @Conditional(Employee.class)
        public ItemWriter<Employee> writer_employee(DataSource dataSource) throws IOException {
            FlatFileItemWriter<Employee> writer = new FlatFileItemWriter<Employee>();
            writer.setResource(new FileSystemResource(FinanceReportUtil.createFile("Employee.csv")));
            writer.setHeaderCallback(new FlatFileHeaderCallback() {
                @Override
                    public void writeHeader(Writer writer) throws IOException {
                    writer.write("id, name");
                 }
             });
            DelimitedLineAggregator<Employee> delLineAgg = new DelimitedLineAggregator<Employee>();
            delLineAgg.setDelimiter(",");
            BeanWrapperFieldExtractor<Employee> fieldExtractor = new BeanWrapperFieldExtractor<Employee>();
            fieldExtractor.setNames(new String[]{"id", "name"});
            delLineAgg.setFieldExtractor(fieldExtractor);
            writer.setLineAggregator(delLineAgg);
            return writer;
        }

        @Bean
        @Conditional(Manager.class)
        public ItemWriter<Person> writer_manager(DataSource dataSource) throws IOException {

            // Does the same logic as employee
        }

        // Also has job and step etc.
    }

It will create the file even with spring.batch.job.enabled=false, to overcome this I have created custom logic to inject the beans or not as below

application.properties

# all, manager, employee
person=manager

ManagerCondition.class

public class ManagerCondition implements Condition {

@Override
public boolean matches(ConditionContext context, AnnotatedTypeMetadata metadata) {
    String person= context.getEnvironment().getProperty("person");
    return person.equals("manager");

}