The company is owned by non-Muslims but there are only one or two of Muslim shareholders.
After buying the beer business, the operations will be at a different site. There will be two sites, the current site will continue to produce soft drinks and the other site will be beer production site. Yes my company will become the parent company and it will manufacture
and sell beer as a separate entity.
In IT dept, I will have to setup computers, communications and programs to run beer business, but I will not be selling it.
You mentioned that this company will soon purchase a beer company and, as a result, will manufacture and sell beer; and you want to know whether it will then be permissible for you to continue working for the company in the IT department.
The answer to this question is that it will be permissible for you to continue working in the IT department of this company after it starts manufacturing and selling beer with two conditions:
1) The majority of the company is owned by non-Muslims.
2) The services you will render for the company are such that they can be used for permissible things too (i.e. apart from being used for selling beer). Hence, the software and programs that you will have to install should be such that they can be used for permissible things too (such as for selling juice and other permissible things). (Note: Since computers and communications devices can be used for permissible as well as impermissible things, it will be permissible to setup computers and communications devices.)
If any of the abovementioned two conditions are not fulfilled, it will not be permissible for you to continue working in the company after it starts manufacturing and selling beer.