Optimizing Large Microsoft 365 Backups with Synology

Real-World Deployments of Large Microsoft 365 Backups Optimized with Synology

Microsoft 365 has become the foundation for email, collaboration, document sharing, and productivity for many charities, schools, and small to medium-sized businesses (SMBs). As organizations grow, the need to protect years of accumulated data across Exchange Online, OneDrive, SharePoint, and Microsoft Teams becomes increasingly important.

One of the biggest concerns when deploying a new backup solution is the initial backup. Organizations with multiple terabytes of Microsoft 365 data often discover that the first synchronization can take many hours or even several days. Initial synchronizations of more than 19 hours have been reported in community discussions, including deployments shared by charities and SMB administrators, for Microsoft 365 environments larger than 4 TB. While this may seem alarming, it is generally a normal part of the initial backup process.

With proper planning and the right Synology infrastructure, organizations can complete large initial backups successfully while minimizing disruption to daily operations.

Why the First Backup Takes Longer

Unlike incremental backups, the initial backup must download every protected item from Microsoft 365.

This often includes:

• Exchange Online mailboxes

• OneDrive files

• SharePoint sites

• Microsoft Teams data

• Shared mailboxes

• Microsoft 365 Groups

Once the initial backup is complete, future backups typically transfer only new or modified data, significantly reducing backup times.

Factors That Affect Backup Speed

Several variables influence how quickly Microsoft 365 data can be protected.

Common factors include:

• Total Microsoft 365 data volume

• Number of users

• Internet upload and download speeds

• Microsoft API throttling

• NAS hardware performance

• Available storage capacity

The larger the Microsoft 365 environment, the longer the initial synchronization will usually take.

Choosing the Right Synology Hardware

Hardware plays an important role in backup performance.

Organizations should consider:

• Multi-core processors

• Adequate system memory

• Enterprise-class hard drives

• SSD cache where appropriate

• High-speed network connectivity

• RAID configurations designed for backup workloads

Properly sized hardware helps maintain consistent backup performance as Microsoft 365 environments continue to grow.

Optimize Storage Before Deployment

Preparing storage before beginning the initial backup helps avoid interruptions.

Best practices include:

• Creating dedicated storage pools

• Planning sufficient free capacity

• Verifying RAID health

• Testing storage performance

• Confirming backup repository availability

A well-prepared storage environment reduces the likelihood of delays during large backup jobs. Manage Microsoft 365 storage growth to improve backup efficiency and scalability.

Schedule the Initial Backup Carefully

The first synchronization generates considerable network traffic.

Many organizations schedule the initial backup during:

• Overnight hours

• Weekends

• School holidays

• Low-usage periods

• Planned maintenance windows

Running the initial backup outside normal business hours minimizes the impact on users and network performance.

Understanding Microsoft 365 Service Limits

Backup performance is not determined solely by the NAS.

Microsoft applies service protection mechanisms that regulate API activity to ensure fair usage across Microsoft 365 tenants.

Organizations may occasionally experience:

• Temporary throttling

• Variable transfer speeds

• Short pauses between operations

• Extended backup times for very large tenants

These behaviours are expected and do not necessarily indicate problems with Synology or the backup configuration.

Monitor Backup Progress

Large backup jobs should be monitored throughout the initial synchronization. Learn proven strategies for scaling Microsoft 365 backups as organizations grow.

Administrators should review:

• Backup progress

• Storage utilization

• CPU usage

• Memory consumption

• Network throughput

• Backup logs

Monitoring helps identify potential bottlenecks before they affect completion times.

Plan for Future Growth

The initial backup is only the beginning. 

Organizations should also prepare for:

• Additional Microsoft 365 users

• Growing OneDrive storage

• Expanding SharePoint sites

• Increased Microsoft Teams collaboration

• Longer retention requirements

Synology’s scalable storage architecture enables businesses to expand backup capacity without replacing their existing infrastructure. See why every business needs a Microsoft 365 backup strategy

Benefits After the Initial Backup

Once the initial synchronization is complete, organizations typically experience:

• Faster incremental backups

• Lower bandwidth consumption

• Shorter backup windows

• Improved recovery readiness

• Simpler backup management

The initial investment in time results in a far more efficient long-term backup process.

Best Practices for Large Microsoft 365 Backups

Organizations can improve backup performance by:

• Selecting appropriately sized Synology hardware

• Planning adequate storage capacity

• Scheduling the initial backup during off-hours

• Monitoring backup progress regularly

• Reviewing Microsoft 365 growth trends

• Expanding storage proactively

These best practices help ensure reliable Microsoft 365 protection while supporting future business growth. Understand Microsoft 365 backup solutions for business data protection

About Synology

Synology Active Backup for Microsoft 365 provides centralized protection for Exchange Online, OneDrive, SharePoint, and Microsoft Teams without recurring per-user backup licensing fees. Combined with scalable NAS storage, Snapshot Replication, Hyper Backup, and centralized management, Synology enables organizations to efficiently protect even multi-terabyte Microsoft 365 environments while maintaining complete control of their backup data. Understand how to Scale enterprise M365 backups with Synology solutions.

About Epis Technology

Epis Technology helps charities, educational institutions, and businesses design and optimize Microsoft 365 backup environments through Synology consulting, storage architecture, capacity planning, backup implementation, disaster recovery strategy, infrastructure optimization, and ongoing Synology support.

By combining deep Synology expertise with practical deployment experience, Epis Technology helps organizations successfully complete large Microsoft 365 backup projects, improve long-term performance, and build scalable backup environments that protect critical business data for years to come.