Yes, you can pay multiple invoices using a single transaction. Please follow below mentioned steps.
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Login to Client Area
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At Home page, under Overdue Invoices, you will have an option Pay Now to make the payment for all due invoices.
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or Go to Billing >> My Invoices
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You will get a button called Pay all on top-left corner to pay all due invoices using a single transaction.
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You will get a single combined invoice for all unpaid invoices. Select the payment gateway from drop down, click on Make Payment button and proceed with the payment.