A little side project I built: <a href="https://www.spotinvoice.com/" rel="nofollow">https://www.spotinvoice.com/</a> that spits out PDF invoices and lets you collect payments via Stripe. No accounting software integration, though.
I'm in the weird position of a freelance audio engineer working mostly on a hobbyist basis. I have 5-6 customers and occasionally 4 or 5 invoices in a month, which means I can't use the free version of anything, but the next step up is designed for a full-time or nearly full-time professional and priced accordingly. I really couldn't justify more than $3 or $4 per month based on my revenue.<p>The only option for me seems to be Zoho Invoice.
I've used <a href="http://getharvest.com" rel="nofollow">http://getharvest.com</a> in the past and I think it works really great. Both on invoicing and time tracking. Haven't tried the payment part though.<p>This hasn't been released yet, it is invite only atm. But at least the site looks pretty good: <a href="http://invoisse.com/" rel="nofollow">http://invoisse.com/</a>
I use LibreOffice to create the invoice, a directory on my computer to keep my local copy, email to send it, and my bank's website to check whether it's been paid. It doesn't have to be any harder than that.<p>Though I rarely send more than one invoice per month. If you send a lot, I can imagine some specialized software may pay off. For me, however, that would be overkill.
If you're looking for an invoicing tool that is completely integrated with your accounting check out Wave.<p>www.waveapps.com/invoicing<p>It is surprisingly free invoicing tool that also accepts credit card payments (powered by Stripe). Wave provides a full featured small business eco-system that you will also likely enjoy.
Harvest seems to accomplish what you are looking for. You'll have to use either Paypal or Stripe to accept payments. And there is add-ons to integrate with some accounting software but you'd to check for your accounting software.<p><a href="http://getharvest.com" rel="nofollow">http://getharvest.com</a>
Checkout <a href="http://invoiceomatic.io/" rel="nofollow">http://invoiceomatic.io/</a> its a free invoice and reminder service provided by <a href="http://ww.freeagent.com" rel="nofollow">http://ww.freeagent.com</a> as part of their marketing, onboarding, but its great and spam free.