As per Section 40A(3), "where the assessee incurs any expenditure in respect of which a payment or aggregate of payments made to a person in a day, otherwise than by an account payee cheque drawn on a bank or account payee bank draft, exceeds twenty thousand rupees, no deduction shall be allowed in respect of such expenditure."
It is very clear from the above that if the aggregate of payments made to the same person on the same day exceeds Rs. 20,000, Section 40A(3) shall be applicable. Also it is immaterial whether they belong to the same bill or different bills.