A customer initiated transaction, or CIT, is any payment the cardholder actively triggers and is present for: a checkout, a one off purchase, or the first payment of a subscription. The customer is in the flow and approves the charge in real time, which is what separates a CIT from a merchant initiated transaction the merchant runs later against a stored card.
Why it matters
CITs are where Strong Customer Authentication and its step up challenge apply, because the customer is present to complete it. That matters most at the start of a subscription: the first CIT of a series is the payment that establishes the credential on file mandate every later merchant initiated transaction relies on. Authenticate that first payment properly and the recurring charges that follow can stay out of scope for SCA. Rush it, store a credential without a clean authenticated CIT behind it, and the MITs built on top are exposed to declines and disputes.