We use Stripe to process all payments made through Shopkeeper.
Stripe has been audited by a PCI-certified auditor and is certified to PCI Service Provider Level 1. This is the most stringent level of certification available in the payments industry.
All card numbers are encrypted on disk with AES-256. Decryption keys are stored on separate machines. None of Stripe’s internal servers and daemons are able to obtain plaintext card numbers; instead, they can just request that cards be sent to a service provider on a static whitelist. Stripe’s infrastructure for storing, decrypting, and transmitting card numbers runs in separate hosting infrastructure, and doesn’t share any credentials with Stripe’s primary services.
See more info on Stripe's security.