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I am fairly new to Sharepoint but I have a software engineering background. I have been charged with branding our companies Sharepoint intranet. We are using Office 365 Sharepoint online. The goal is to edit the master page to have a custom Header (site navigation) and footer. But the more I read on this process, the more confused I become. Apparently, we are not supposed to edit the master page anymore, with the reason being that any customizations could break if MS updates the Sharepoint Online? Does this rule also apply to Publishing style templates or just teamsites? I guess the main question is:

What is the best workflow to have custom (global)navigation (change CSS type items), and a custom footer, for a Office 365 Sharepoint Online site?

The current top site in the site collection carries a Publishing style template. Ideally, I would want any subsites(regardless of the chosen template) to inherit the header and footer to provide consistency throughout the user experience.

Any links, workflows, or advice would be greatly appreciated!

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The general guidance from the PnP group is not to customize the master page if at all possible, but know the limitations if you do, for the reasons you've given. By customizing, you are potentially breaking any new features and changes that are released. You have to be vigilant of changes and try to incorporate them into your design.

There are ways to achieve a branded design without master page customization. This can be achieved through using the Alternate CSS file link to provide your own style sheet to the site collection. You can use UserCustomActions to staple additional JS files to your site (or web) to add additional functionality like jQuery, Bootstrap, or the like. You can use custom page layouts to provide layout options as desired.

My personal opinion on the matter is if you want a highly branded intranet, SharePoint Online is not the right place. It should be something that lives on prem. All the changes they are making to the service, like modern sites and lists, the emergence of Office Groups, mean you are wasting a lot of time and money trying to stay up to date with changes they make to the service. It is better to keep that in house where you have total control over the environment and can thoroughly test SharePoint upgrades against your design.

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Eric's answer is really good (+1), and the points he makes about PnP recommendations are valid, but I disagree somewhat with his conclusion that you should never do them in O365. If you go the on-premises route, unless you already have a great deal of SharePoint admin experience in house, you will merely be trading those problems in for a new set of potentially more serious problems.

I've done a number of O365 intranets now - close to ten I'd say - and yes, there are challenges, and sometimes Microsoft will break the things you've built, but there are also great opportunities. Delve, for instance, is a phenomenal and under-used tool that can bring great value to an intranet. But yeah, stuff breaks now and then, as Eric noted, and you need to be quick to mitigate the damamge when that happens.

Publishing sites are probably the one area of O365 where it might still make sense to develop custom master pages, and in the real world organizations still do this all the time. The new "Modern" experience does not yet offer enough flexibility to be a compelling solution on its own, so if the master page route is the only way you can meet your requirement I'd say do it. But just know, over time the new paradigm will mature, and a tipping point will be reached. When that time comes, be prepared to pivot.

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