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The Pay Now option is not visible on the online page of an invoice when the currency of the invoice does not match the organisation's default currency. This is especially annoying when Payment Services such as Stripe are set-up as they can easily process multiple currencies.

Moreover, as it is not (or poorly) documented that Payment Services are not usable when using a foreign currency, it just seems to be a bug. I contacted support who responded with the following:

"The Pay Now button on an invoice only shows if the currency of the invoice or payment account is the same as your organisation's base currency."

Our default currency is AUD, but most invoices are in USD, in general payments are collected directly in Stripe, but it is essential for us to be able to create a USD invoice in Xero and get it paid directly as it is possible in AUD.

Thanks!