What happens if the customer pays only after the e-Invoice has been submitted (e.g., 1 month later)? Does this affect the e-Invoice?

No, it doesn’t affect the e-Invoice.

When you issue an e-Invoice, it is submitted to LHDN at the time of invoice issuance. The e-Invoice is validated and becomes a legally recognized document regardless of when payment is received.

You issue the e-Invoice based on the invoice date (e.g., 1 July), and the customer may pay later (e.g., 1 August); there's no need to update or resend the e-Invoice after payment—just record the payment in your accounting system for reconciliation.

** Exception: If there's additional charges that affects the original amount, you may need to issue a refund note, credit note or debit note type e-Invoice to reflect the adjustment.