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We are rolling out SharePoint to our organisation and have kept the default, whereby docs open in the web app. We have had a number of teams asking us to change the default for their sites so that docs open in the desktop instead. I am trying to find out if there are any drawbacks/risks associated with changing this default setting?

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This is a topic is is close to me so I thought to mention a few thigs.

#1 - there is no right way

some people like to have it open in the browser, some people prefer the client application.

my recommendation is to pick a convention for most sites and then allow for some exceptions if the business requires it.

#2 - avoid library-level open behaviour

while you can use the library level setting 'Default open behavior for browser-enabled documents', this is best kept to 'Use the server default'. this is because you can control this at the site level enabling or disabling the feature 'Open Documents in Client Applications by Default'.

if you start playing with the library level, it will become much more difficult to control and change the behaviour between one and the other (meaning having to parse all libraries in the site)

side-node: last time I checked, we could NOT set the library setting BACK to 'Use the server default'. so if you happen to change it, you cannot programatically revert it back to default, only using the UI (if anyone found a way, let me know in the comments!)

$list = get-pnplist "mylist"
$list.DefaultItemOpenInBrowser = $false #open in desktop
$list.DefaultItemOpenInBrowser = $true #open in browser    
$list.DefaultItemOpenInBrowser = ??? #use server default
$list.update()
invoke-pnpquery

#3 - implement slowly / test

don't just change the behaviour for 500 sites in one go. change 1, change 10. ask the users to test. give it some time to marinate.

#4 - write documentation

prepare an article explaining the change. send it to everyone and/or send it whenever someone reaches out about the change

#5 - pros and cons

we cannot talk about the default open behaviour without talking about the default open mode. in the past, documents opened in the browser in view-only mode, but now they open in edit mode.

this is probably an argument in favor of the desktop mode because the moment you open a document in edit mode you trigger coauthoring and with it, potential document locking.

#5.1 scenario - signing

a document needs to be signed. user A opens the document in the browser. user A cannot sign because the browser doesn't support this feature, but now user B cannot sign it in the desktop app because user A has a session open. this wouldn't be a problem if user A opened in the desktop in the first place

#5.2 scenario - office availability

imagine you share a document with an external and they don't have office installed at all. documents are set to open in the desktop app by default. externals will struggle to get the document open

further comments

changing the default open behaviour from browser to desktop should be fine in the context of an enterprise environment with mostly internal users with office licenses. in fact, I would say it's not only ok but desireable. but there will be cases where that will not work, and for those you can have exceptions (site or library level). just make sure those exceptions don't get out of hand.

for implementation details and other information you can check here, https://www.sharepointdiary.com/2018/03/sharepoint-online-open-documents-in-client-applications.html

other apps

other applications such as teams and outlook might have a life of their own. you'll need to test and see how they behave and if you want to change anything there as well.

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