Hi,
We're dealing with the same problem after our Magento migration. Did you find out what caused the organic drop?
Looking forward to hear from you 
Posts made by DocHorse
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RE: On site issues after Magento 2 launchposted in On-Page Optimization
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SEO rank down after Magento migrationposted in Intermediate & Advanced SEO
Since November we migrated our shop from Magento 1 to 2 and our organic traffic has dropped by 50%. We still haven't figured out the cause (or a solution). Are there more Magento users who have the same issue?
Charlotte (www.dochorse.nl)
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RE: SEO rank down 35%posted in Intermediate & Advanced SEO
Hi
Since November we migrated our shop from Magento 1 to 2 and our organic traffic has dropped by 50%. We still haven't figured out the cause (or a solution). But our developer has found out that Magento 2 handles Javascripts in a different way which causes a very bad result at Google PageSpeed Check. We have been in contact with magento and they advise to partly bundle Javascripts and partly offer separate files. Have you also had this problem? Is your organic traffic back to the level it was before the migration?
Charlotte (www.dochorse.nl)