Tailor-made for own requirements:
Perhaps, the most significant benefit of custom software development is that it is custom made as per your company requirements and standards in order to best serve your business needs. Also, it saves money on buying licensed softwares from the market which we later find that they don’t serve that much usability or have the full features that we required.
More Scalable:
Custom software’s are more open-ended and can be modified further in the house to serve your own business purpose. Also, the people who will do your custom software will maintain it as long as your business grows, as they work on a contract basis. Plus an off the shelf software might not work with a large or scale business whereas a custom based software is exactly as per the business you have.
External Threat Protection:
Custom softwares are less vulnerable to hackers as they have their own code made from scratch. Whereas, shelf based softwares are known to the market and hackers know their vulnerabilities already. So a custom based software will be a much less attractive target for most hackers than a shelf based one, and they might have to perform more effort to know how to breach the system.
Compatible with existing running 
softwares:
Custom software’s are made such as to co-exist with the software packages you are using already. However, there are bound to be some or the other issues, but one can minimize them if using a custom based software. Compatibility can lead to your employee’s productivity getting low due to them experiencing continuous errors. With custom based software system you can avoid this problem.
Maintenance:
Your custom software can be maintained by you as long as you want it to be maintained. In case of a shelf bought software, you better buy it from a reputed company with long life expectancy, or you might not get any maintenance if the company goes out of business or bankrupt. Also, you might face dire consequences with your business if you ever needed a change in your software urgently. This will ultimately save your money or any sudden expense that might come.
Save on hardware acquisition:
Licensing software requirements may contain installing and buying extra hardware to support it and run it effectively. Custom software may be developed as per, taking into consideration your hardware capabilities, such that you don’t need to buy any new hardware.
All in all, custom software provide an excellent base to build upon.