How to Overcome the Top 5 Challenges of Managing Microsoft 365

Written by: Thomas Laciano

Updated: 09/20/2021

Over the past year, Microsoft Teams has owned the spotlight in the Microsoft world due to rapid and significant adoption in the marketplace — Microsoft reported a whopping 115 million daily active users in October of 2020. But with all the focus on this single app, it can be easy to forget that Teams is only one piece of the extensive Microsoft 365 (M365) puzzle. It is important to recognize and address the challenges of managing Microsoft 365 as a whole.

While Microsoft Teams is quickly becoming the main hub for work for many employees, this functionality is really driven by the numerous applications that make up the M365 ecosystem. The incredibly integrated nature of Microsoft 365 — both for employees using the apps and IT teams handling administration — makes the system extremely powerful but also difficult to manage. 

In this blog, we’ll cover why a well-managed Microsoft 365 instance is important, the top five challenges of managing Microsoft 365, and how a Microsoft Managed Services Provider can help set your company up for success. 

Why a Well-Managed Microsoft 365 Instance is Important

Why a Well-Managed Microsoft 365 Instance is Important

The Microsoft 365 ecosystem is comprised of numerous apps that cover everything from email and chat to project and task management to security and automation. The full list of applications includes: 

  • Microsoft 365 Apps: Word, Excel, PowerPoint, OneNote, Publisher, and Access 
  • Email and Calendar: Exchange, Outlook, and Bookings  
  • Meetings and Voice: Microsoft Teams  
  • Social and Intranet: SharePoint and Yammer  
  • Files and Content: OneDrive for Business, Stream, Sway, Lists, and Forms 
  • Work Management: Planner, Power Apps, Power Automate, Power Virtual Agents, and To Do 
  • Advanced Analytics: MyAnalytics and Power BI Pro  
  • Viva: Topics, Connections, Learning, and Insights 
  • Microsoft 365 Groups 
  • Microsoft Advanced Threat Protection 

Business users rely on these apps to complete their work as efficiently and effectively as possible. For instance, end users count on Outlook and Teams to communicate and meet with colleagues, vendors, and clients and need to be able to store and retrieve information from SharePoint and OneDrive. As many companies look to improve employee experience and engagement for their workforce, applications like Yammer and the newly announced Viva will increase in importance. 

Because end users rely on so many different applications in the M365 stack to support their day-to-day work activities, it is crucial that these platforms are available and useful. The out-of-the-box settings may not work for all — or even a majority — of companies and their employees. When these solutions are not actively managed or reviewed against end-user needs, they can become a barrier to productivity and can potentially also lead users to implement shadow IT solutions without the IT team’s knowledge. Ultimately, this can create significant difficulty for IT teams as they try to reign in content sprawl and respond to requests from end users trying to find a tool to fit their needs. 

To get the most out of these applications, IT teams must overcome the challenges of managing Microsoft 365 in such a way that ensures content is not only available to employees but also structured in a way that makes it easy to find and use. On top of that, it is necessary to review all back-end settings and policies to find the right balance between security and governance and employee productivity.

The Top 5 Challenges of Managing Microsoft 365

The Top Five Challenges of Managing Microsoft 365

Because Microsoft 365 is not just a single app but rather an entire suite, there are a variety of different challenges IT teams face when it comes to management. These challenges of managing Microsoft 365 are often compounded for enterprise-sized businesses, because they tend to have complexities that smaller companies don’t have to contend with. For example, different organizations within one enterprise may have competing needs or there may be geo-political differences in how features are enabled or disabled. 

The top five challenges of M365 management are troubleshooting, user adoption, security, IT utilization, and performance. 


To say that determining the root cause of a Microsoft 365-related issue can be challenging is an understatement. Because M365 is comprised of so many various but interconnected apps, a huge amount of data is generated every day. But deciding what to focus on is just the first hurdle when it comes to troubleshooting — next comes navigating the myriad of Microsoft admin centers to track down the root cause and implement a solution. 

User Adoption 

Creating buy-in from end users as well as tracking adoption of Microsoft 365 applications can be tricky and a resource drain on the IT team, especially when transitioning from an on-premises solution. If M365 services aren’t fully adopted, it can also cause issues when it comes time for IT to show the ROI of this solution. While the native Microsoft 365 admin tools can give IT some insights into adoption, it can still be a challenge to understand the full picture across the entire M365 suite. 

Security Challenges of Managing Microsoft 365

Although Microsoft provides multilayered security for M365, many organizations are still concerned about losing data that’s stored in the cloud. To add to the confusion, navigating the Microsoft security model is anything but simple and requires in-depth knowledge of at least five different admin consoles. Some security settings for certain apps can be set in one single place, while others have overlapping functionality with other applications. Microsoft offers security-related settings to protect customer data, but many require a heavy handed “all-or-nothing” approach causing significant frustration for end users. For certain apps like Teams, this native security and governance functionality just isn’t flexible enough to meet the needs of most enterprises. But it’s crucial to overcome this challenge of managing Microsoft 365. 

IT Staff Utilization

With all of these applications and corresponding admin consoles, the most effective and efficient way to proactively manage Microsoft 365 can be unclear — especially for small IT teams, often reduced due to outsourcing to cloud services. An ideal team includes an expert in each application or subject area, but this can be cost prohibitive even for large enterprises. No matter the size, every IT team faces the additional challenge of managing their existing M365 deployment while also trying to stay up to date with the pace of new solutions and features released by Microsoft. 


At the end of the day, it isn’t enough to simply deploy Microsoft 365 and educate your end users — the system must be monitored on an ongoing basis for performance issues, anomalies, and usage. Most often, monitoring performance is an issue of bandwidth for IT. Every application generates thousands of data points that must be combed through to glean insights into performance, and it can take even more time to determine correlations between these points. And that’s before Help Desk tickets are taken into account! 

Gain a simultaneous, panoramic view of all collaboration and communications platforms, expediting responses to service interruptions and threats.

To address all these top five challenges of managing Microsoft 365, companies must take a multifaceted approach. It is key to build a team of subject matter experts for critical technologies in the M365 stack. Exactly which applications are most critical can vary from business to business, but typically Exchange, SharePoint, and Teams are at the top of the list. Additionally, it is crucial to understand your company’s need for advanced features such as legal hold and telephony services or integration. These services may require the identification of additional team members or a more highly skilled subject matter expert. 

Even after your team of experts has been established, an ongoing investment in training is necessary to keep up with advances in existing services as well as the introduction of new services. Consider the impact of Microsoft 365’s Power Platform and the recently introduced Viva offering. Both are powerful apps that can have a positive effect on a business’ bottom line but require new skills and knowledge from the IT team to be implemented and managed correctly.

How a Microsoft Managed Services Provider Can Help

How a Managed Services Provider Can Help with Challenges of Managing Microsoft 365

For many companies, addressing all of the challenges of managing Microsoft 365 in-house doesn’t have the right return on investment or simply isn’t viable. This is where a Microsoft Managed Services Provider (MSP) can help. 

Microsoft 365 MSPs offer 24x7x365 coverage for end-user support and fulfillment of service requests for Teams, Exchange, SharePoint, OneDrive, and the many other applications included in the M365 service. The engineers on staff with an MSP have typically earned certifications from Microsoft specific to M365 services and are well-versed in the ins and outs of each application. 

The Benefits of Using a Microsoft 365 Managed Services Provider

There are multiple benefits to using a Microsoft 365 MSP compared to keeping all management in-house. The most obvious are cost benefits — many companies can outsource all management of their Microsoft 365 instance for far less than they would pay a comparable full-time in-house team. That said, if your company is considering using a Microsoft 365 MSP, make sure to designate an existing full-time employee who is accountable for understanding the technology and strategic direction of the business and can act as the primary point of contact for the MSP. Without this in place, you may lose the ability to challenge the MSP should you feel they are acting in their own best interest rather than for your company. 

Another benefit of using a Microsoft 365 MSP is increased access to Microsoft support. In addition to your own Microsoft Premier contract, an M365 MSP will also have a partner support contract with Microsoft. This allows for the escalation of issues or bugs that have been found across multiple tenants and will enable you to handle the larger challenges of managing Microsoft 365. 

What to Look for in a Microsoft 365 Managed Services Provider: Experience in Challenges of Managing Microsoft 365

When looking for a Microsoft 365 Managed Services Provider, it’s best to seek one with a “trusted advisor” model that will act as a true partner to your company. When operating with this model, the MSP will always work to do what is in the client’s best interest — including going above and beyond contractual obligations. Make sure to also ask about the MSP’s engineers — what level of experience do they have and how long have they been with the MSP? The more experience engineers have and the longer they stay with the MSP, the more value they can provide to clients. 

You may also want to take into account the specialization of each M365 MSP. Some provide broad product coverage while others have depth in specific areas. Which one is right for your company depends on current needs and future goals. For instance, if your company has a goal to improve employee communication, productivity, and engagement it may be best to choose an MSP with specific experience with Teams, Outlook, Yammer, Viva, etc. 

Just as there are things to look for in an M365 MSP, there are also things to avoid. To start, keep an eye out for companies who really act as consultants but may be masquerading as a managed service provider. Enterprises should also be wary of MSPs where part or all of the body of work is further subcontracted. If the work is outsourced once it could be outsourced again, and this inevitably reduces the quality of work. Additionally, avoid MSPs that will not sign results-oriented service level agreements. If they won’t share in the risk, will they really care about the outcome? Your challenges in managing Microsoft 365 might not be handled to your liking. Similarly, don’t focus on small penalties — choose a partner that will ensure you are both successful. 

Our expert consultants can work with you on platform selection and create deployment plans to ensure a successful roll-out.

Unify Square’s PowerSuite Cloud Managed Services for Microsoft 365 improves the user experience and untangles the complexities of M365 for IT. By working with our clients as a true partner and combining our PowerSuite software, certified operations engineers, and processes, we help enterprises deploy, monitor, and manage their Microsoft 365 instances. 

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