I have my bank account linked to Quickbooks but one transaction is not coming through to Quickbooks despite the balance indicating the deposit has been made, any ideas?

Thanks for posting in the Community, rowan-evans83-gm. 

We can do a manual update to have your transactions downloaded in QuickBooks Online. Let me show you how. 

1. Go to the Banking menu or Transactions menu.
2. Go to the Banking tab.
3. Select Update.

Once done, kindly repeat the same steps for at least 3 times and another in the next 24 hours to allow the bank to regain its connection.

This updates all your connected bank and credit card accounts. The number of transactions in each account tile will increase if QuickBooks downloads new transactions.

For your reference, you can check on this article on what to do if you get a bank error or can't download transactions in QuickBooks Online. 

Feel free to drop a comment below if you need further assistance. Have a nice day!