Automated payments and invoicing for web app?

So I'm thinking of starting my own side project, think of it as a job board/craigslist for a specific niche. Employers will be able to post job ads for some fee. I would like this to be as automated as possible, which includes automating the payment and invoicing process.

I will probably code the whole web app myself, since I'm a programmer, but I'm not sure how to do the actual money exchange part. I was thinking of using Stripe for the payments, but how do I issue invoices? Since I'll be collecting money from businesses, they'll all probably need invoices. Is it common to code your own solution, which sends them a PDF after the Stripe payment goes through? Or perhaps there are some services (like Freshbooks or Quickbooks) which I could integrate with through an API?

Any advice would be greatly appreciated.

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