However, just being private doesn't eliminate Stripe's other challenges.
In his interview on "Squawk Box," John Collison highlighted the growing complexity of financial compliance and said banks are becoming more conservative in their partnerships with fintechs.
“We have started to see the financial system become more involved in financial policy enforcement,” Collison said. "And then you tend to get these occasional flare-ups from time to time."
Both Wells Fargo and Goldman Sachs have distanced themselves from the company, according to The Information, prompting Stripe to turn to Deutsche Bank and other institutions for key services. Collison didn't provide details to CNBC, but acknowledged that Stripe has had to navigate shifting relationships.