Today I finally was able to setup a custom theme for my Office 365 Navigation Toolbar! It is very easy to do this, log into your Office 365 tenant as a global admin.
In the upper right had corner under your picture you should see your company name, in my case it is ‘Office 365 Evangelist’, click on this link
From there select the Custom Theming option on the left hand side and go for it!
As you can see above, I customized my Nav toolbar in honor of my favorite NFL team, The Denver Broncos!
At the bottom of the page ensure you Save the changes.
I went back to my Admin Portal and unfortunately the changes to the Nav toolbar did not stay!
So I got to thinking, I set my custom theme in OWA to the circuits some time ago as you can see above. So I went the the OWA/Outlook link and selected the gear to change my custom theme back to the top left ‘Blue’ color and that immediately switched the Nav toolbar to my custom theme I set. See below.
Great, now OWA is using the custom theme, but I again went back to the Admin Portal and still had the circuits theme. Back to the gear by my picture, I selected Change Theme and it brought me to the below area and selecting the ‘Orange’ block in the upper left immediately switched to my custom theme!
So now I am all good, all toolbar links now use my custom theme except for Yammer!