Salesforce1 app is nice, it gives you access to your Salesforce data and application with no cost and lower effort to configure. But in some organization, it has to be off due to compliance guidelines or security protocols, administrators may be asked to prevent all User from accessing the Salesforce1 platform.
To completely eliminate your Users' ability to access the Salesforce1 interface, you will need to make the following changes:
1. Connected Apps
Navigate to Setup | Apps | Connected Apps | Manage Connected Apps, click Edit link on Salesforce1 for Android, Salesforce1 for iOS, and Salesforce1 for Windows.
Ensure that the 'Permitted Users' value under 'OAuth policies' is set to 'Admin approved Users are pre-authorized', and click Save.
2. Deactivate from User Profile
Navigate to User Profile and ensure that the 'Salesforce1 for Android', 'Salesforce1 for iOS', and 'Salesforce1 for Windows' permissions are all disabled under the "Connected App Access" section. Once all of these have been disabled, save the changes for the Profile and repeat these steps for all Profiles in your organization.
3. Salesforce1 mobile browser app
To ensure that your Users are not able to access the browser-based version of Salesforce1, navigate to Setup | Apps | Mobile Apps | Salesforce1 Settings. From here, ensure that the 'Enable the Salesforce1 mobile browser app' option is unchecked, and click Save.
Now, let's see what happened when user login to Salesforce1
Next, we need to enable Salesforce1 for a few users to test if Salesforce1 can be approved as the corporate-wide app. There are 2 options:
If all the users are located under the same profile, open the profile and look for Salesforce1 under 'Connected App Access'.
2. Permission Set
This would be more flexible as you can enable it user by users across profiles. Ideally, you should create new Permission Set, click 'Assigned Connected Apps', click Edit button and look for Salesforce1 for... and lastly assign the permission set to the users.
Reference: Salesforce1 - How to Prevent all Users from Accessing the App