Is there a way to integrate Paypal checkout with Clickfunnels? instead, the link redirects being used now.
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With a basic PayPal account, you can’t do that and have never been able to do it. On any shopping cart product. PayPal always takes you to PayPal (where they have the SSL and control) and then takes you back to the originating site.
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You’ll have to create a new BUY button at Paypal side, and then get the link (or the code, depending on which you prefer best). Afterward, whenever a user clicks your button within Clickfunnels instead of taking them to the internal order form step, take them to the link Paypal gave you.
You’ll have to add a return URL to your Paypal configuration, to take your clients once the finish purchasing back to the next funnel step to (maybe) upsell them more.
Please notice: Using Paypal is way not recommended, especially when having Upsells/Downsells in your funnel. Testing has proven that Paypal can really damage your conversion rates.
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That has been solved “finally” 
check out this thread:
it has everything you need to know about smoothly integrating Paypal into your sales funnels without damaging your ROI.