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I have an ecommerce store built with an external vendor on a different URL than my main site.

If I add a link to the store in the navigation of my main site, will this be seen as malicious by Google and hurt my SEO since it's an external link and from an outside source?

I guess I would just like to know what the pros and cons of this would be.

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No it will not seen as malicious - IF the linked site is not a "bad neighbour". Although it will have an effect on SEO as it is an outgoing link on every page, which the crawler will follow.

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