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As of 2.1.0-rc2 stripe-node supports passing Stripe Connect access-tokens on a per request basis:
2.1.0-rc2
stripe.RESOURCE.METHOD([params...][, ACCESS_TOKEN][, callback]);
For example:
stripe.customers.update( yourCustomerId, { description: 'Updated description here' }, accessToken, // Gained from the Connect OAuth POST function(err, updatedCustomer) { // ... } );
Read more about integrating Connect OAuth flow.