Because Shopify doesn't support an automatic download you will need to add your Shopify account as a bank account manually.
To add your Shopify account:
1. Under the Banking tab, click Accounts. Then, click the New Bank button.
2. Click the Click here to import Bank transactions link to import Bank transactions.
3. Under Bank Name type Shopify and put in 1111 for your account number. You can leave the account type set to Checking. Then click Next.
4. On the Upload Bank Transaction page, click Cancel.
5. On the screen showing your bank account information, click OK.
6. If you are asked if you would like to associate this account with your Primary Checking account click Cancel.
7. You are done! You have successfully added your Shopify account.
Now you can Download your Shopify transactions.