SQL Server 2016 Compliance Risks: What You Need to Know After End of Support
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02 May, 2025, 17 min read
SQL Server 2016 is out of time. Microsoft has officially ended support, which means no more security patches, no bug fixes, and no guarantee of compliance. That puts your systems and business at risk.
Moving to Azure is a smart way to improve security, streamline operations, and prepare your infrastructure for the future.
By moving SQL Server 2016 to Azure, you can:
Still, the migration isn’t plug-and-play. You need to pick the right destination and move with care to avoid downtime or data loss.
That’s where Atlas Systems comes in. We help healthcare organizations, financial firms, and enterprise teams plan and execute SQL Server migrations with precision, using proven tools and processes to keep things running smoothly.
This guide walks you through:
Sticking with SQL Server 2016 is a security gamble that holds your business back. Now that Microsoft support has ended, your infrastructure is exposed to performance issues, compliance gaps, and higher operating costs.
Moving to Azure is a chance to clean up technical debt, eliminate waste, and get ready for what’s next.
Here’s why more IT teams are making the move:
Without support, SQL Server 2016 is vulnerable, and that’s a dealbreaker in industries like healthcare, finance, and insurance. Azure comes ready with:
It helps meet HIPAA, GDPR, PCI DSS, and other frameworks without the constant patch-and-pray approach of legacy systems.
Forget hardware refresh cycles, surprise outages, and time spent chasing patch schedules. Azure handles:
Your IT team can finally focus on high-impact work without the need to babysit outdated servers.
With Azure, you can scale resources up or down in real time. Use Azure Hybrid Benefit to bring your existing licenses, and reduce spend further with Reserved Instances for predictable workloads.
You get control, flexibility, and smarter budget planning.
In addition to keeping your databases running, Azure plugs you into a larger ecosystem:
Modernizing your data infrastructure opens the door to innovation without starting from scratch.
Atlas Systems has helped large health systems and regulated enterprises move off legacy SQL environments with zero data loss and minimal downtime. Our blueprint includes end-to-end assessments, clear cost modeling, and hands-on execution that works in real-world conditions.
SQL Server 2016 had a good run. But Azure is built for the challenges you’re facing now and the ones you’ll face next.
There’s no one-size-fits-all approach to moving SQL Server 2016 to Azure. Microsoft offers three main deployment options, and picking the right one depends on how much control you need, what features your applications rely on, and how ready you are to modernize.
Here’s how they break down:
This is Microsoft’s fully managed database platform designed for speed, simplicity, and scale. Choose this when your goal is simplicity and scalability.
Best for:
Good fit if you:
What you get:
Limitations:
Avoid if you:
A middle ground between full control and full automation. It offers near 100% compatibility with on-prem SQL Server minus the infrastructure headaches. It’s a good fit for most migrations.
Best for:
Good fit if you:
What you get:
Limitations:
Avoid if you:
This is SQL Server running on a virtual machine you manage, just like your current environment, but in the cloud. This is the right call when you need full control — even if it means more manual effort.
Best for:
Good fit if you:
What you get:
Limitations:
Avoid if you:
Requirement |
Azure SQL Database |
Managed Instance |
Azure VM |
Fully managed |
✅ |
✅ |
❌ |
Full SQL Server feature support |
❌ |
✅ |
✅ |
OS-level customization |
❌ |
❌ |
✅ |
Best for lift-and-shift |
❌ |
✅ |
✅ |
Minimal admin overhead |
✅ |
✅ |
❌ |
Cloud-native optimization |
✅ |
⚠️ |
❌ |
⚠️ = Partial support or more configuration required
Tip: The more legacy features you rely on, the more likely you’ll need Managed Instance or IaaS. But if you’re starting fresh or ready to modernize, PaaS is the leanest path forward.
Not sure which one of the above fits? Atlas Systems runs workload assessments that go beyond compatibility, factoring in performance, licensing, and long-term growth. Our migration team conducts a feature-by-feature assessment, reviews integration points, and maps your current SQL Server setup to the Azure model that fits best — technically and financially.
The right Azure destination is only half the equation. The other half is using the right tools to assess, plan, and move your databases with as little disruption as possible.
Here are the tools that should be in your migration toolkit — all backed by Microsoft, and used extensively by the Atlas Systems migration team.
Purpose: Compatibility check before you move
What it does:
When to use it: Early in the planning phase. It helps you know what’s PaaS-ready, what needs work, and what should be moved as-is.
Purpose: The engine that moves your data
What it does:
When to use it: For production environments where uptime matters. Online mode keeps changes synced during migration, reducing disruption.
Purpose: Migrate from non-SQL systems
What it does:
When to use it: If you’re consolidating systems or switching from a different database engine entirely.
Purpose: Full environment discovery and planning
What it does:
When to use it: For large-scale migrations with multiple SQL instances, VMs, or hybrid environments.
These tools work best when you know exactly how to apply them. Atlas Systems helps clients run DMA and Azure Migrate assessments across dozens of SQL instances, prioritize migrations by business impact, and use DMS to migrate with zero data loss—even in complex, regulated environments.
Pro Tip: Use DMA for your initial scan, then layer in Azure Migrate for cost and capacity planning. When ready, hand it off to DMS for the actual cutover.
Jumping into migration without a plan is asking for downtime, data loss, or worse: regulatory blowback. A structured pre-migration checklist helps reduce risk, improve timelines, and keep stakeholders aligned.
Here’s how to prepare for a smooth move from SQL Server 2016 to Azure:
Why it matters: Knowing what you have and what it touches avoids surprises during migration.
Why it matters: Azure isn't one-size-fits-all. A feature scan early saves weeks of cleanup later.
Why it matters: Picking the wrong model leads to rebuilds, not upgrades. Get it right the first time.
Why it matters: Even well-run migrations need a safety net. Don’t skip this step.
Why it matters: If users or apps can’t reach the database post-migration, the cutover fails.
Why it matters: Migrations don’t happen in isolation. Keep people in the loop to avoid delays.
A solid plan is essential but execution is where things get real. And messy. These field-tested best practices help keep downtime low, data safe, and everyone on the same page.
Your database is live in Azure. The hard part’s done, but don’t hit autopilot yet.
The real value of cloud migration comes after cutover. This is your chance to fine-tune performance, lower costs, and strengthen security. Here’s how to make the most of your new setup.
Why it matters: Azure handles a lot, but tuning is still your job. Slow queries cost money and trust.
Why it matters: Azure is pay-as-you-go — and overprovisioning adds up fast.
Why it matters: Just because you’re in Azure doesn’t mean you’re secure by default. Lock it down.
Why it matters: The database may be fine — but if your reports break, users won’t care.
Why it matters: Azure gives you better tools — now’s the time to use them.
Atlas Systems works with clients post-migration to fine-tune cost, monitor usage, and adjust performance tiers. We help avoid overpaying and underperforming — two of the most common post-move mistakes.
Migrating off SQL Server 2016 isn’t just reacting to Microsoft’s support deadline. It’s a chance to fix what’s outdated, remove the manual effort, and finally align your data strategy with your business goals.
Azure gives you flexibility, security, and long-term cost control — but only if you plan it right.
Whether you're aiming for:
The move to Azure sets the stage for all of it.
We’ve helped enterprises, health systems, and compliance-heavy organizations modernize with confidence. From the initial assessment to cutover and post-migration tuning, we’re with you at every step.
If you’re still running SQL Server 2016, now’s the time to take action — before downtime, audit gaps, or performance issues force your hand.
Let’s map out your path to Azure — and get it right the first time.
Contact the Atlas Systems team to get started.
You can migrate to Azure SQL Database, Azure SQL Managed Instance, or SQL Server on Azure Virtual Machines. Each option fits different workloads and control needs.
Not exactly. Azure SQL Database is a managed platform with fewer features than full SQL Server. For full compatibility, Azure SQL Managed Instance is a better fit.
Yes. Using Azure Database Migration Service (DMS) in online mode allows continuous sync, enabling low or zero downtime during migration.
Use Data Migration Assistant (DMA) to assess, Azure DMS to migrate, and Azure Migrate for infrastructure planning and cost estimates.
Use auto-scaling, reserved instances, and Azure Hybrid Benefit. Monitor performance with Azure Monitor and right-size resources regularly.
Azure SQL Database is best for new, cloud-native apps. Managed Instance offers near-full SQL Server compatibility with fewer admin tasks.
Not always. With Azure SQL Managed Instance or Azure VMs, you can lift and shift with minimal changes. Some legacy features may still need adjustments.
Yes. Atlas has delivered successful SQL Server migrations for enterprise and healthcare clients, focusing on compliance, performance, and zero data loss.