Microsoft Email Back-up in the Cloud

I understand that that the Microsoft licence that my organization is using only guarantees email back-up in the cloud up to 90days. If someone uses MS Outlook web only is it possible that we cannot not get email messages more than 90days? Does requiring all employees to install Microsoft Desktop app or mobile App guarantee the full mail file with say two years data? Let me know if someone in the forum has faced similar situation and how they resolved it.