TL;DR: An SCCM alternative should simplify endpoint management without SCCM’s infrastructure overhead. Modern MSPs need cloud-based tools that integrate RMM, PSA, and patching in one platform. The right solution reduces complexity while supporting both on-premise and remote device management at scale.
Microsoft’s System Center Configuration Manager (SCCM) built its reputation on Windows endpoint management for single-organization IT departments. For MSPs managing multiple client environments, SCCM’s on-premise architecture breaks down. Each client needs dedicated servers, SQL databases, and management points. Training new techs takes weeks instead of days. Windows-only support forces you to run multiple tools for Mac and Linux environments.
This guide examines SCCM alternatives built for MSP workflows, covering what makes endpoint management different when you’re managing dozens of client environments simultaneously and how modern tools address SCCM’s biggest pain points.
Why MSPs are moving away from SCCM
SCCM worked well when IT departments managed single, centralized networks with Windows-only environments. MSPs face different constraints.
Infrastructure overhead
SCCM requires dedicated servers, SQL databases, and management points at each site. The minimum viable setup includes a primary site server running Windows Server, SQL Server Standard or Enterprise (depending on managed device count), WSUS for patch management, and distribution points for content delivery. For MSPs juggling 20, 50, or 100 client sites, replicating this infrastructure becomes unmanageable.
Each deployment needs initial configuration of boundaries, boundary groups, and client settings. Updates consume staff time since you’re patching the patch management infrastructure itself. Hardware failures multiply across your client base, and troubleshooting SCCM issues requires maintaining expertise in Windows Server, SQL administration, and Microsoft’s specific architectural choices.
Cloud-based alternatives eliminate per-site infrastructure. Deploy lightweight agents to endpoints (typically 50-100MB), manage everything through a web console, and scale without adding servers. When a client adds 50 new endpoints, you install agents and start managing devices within minutes instead of provisioning new infrastructure.
Learning curve and training costs
New technicians need weeks of SCCM training before they’re productive. The interface assumes you understand Microsoft’s specific terminology and architectural concepts. Task sequences aren’t just scripts; they’re multi-step deployment workflows with dependencies, conditions, and specific ordering requirements. Distribution points require understanding content library structure, package distribution, and bandwidth throttling. Boundary groups determine which management points and distribution points clients use based on network topology, but the logic isn’t intuitive.
Then there’s the query language. Want a list of devices missing a specific patch? You’re writing WQL queries against the SCCM database. Need custom reports? Learn SQL Server Reporting Services. These aren’t skills techs pick up in an afternoon.
Modern RMM platforms use intuitive interfaces that techs can learn in days, not weeks. Filtering device lists uses dropdown menus and search boxes, not query languages. Deploying patches means selecting which updates to approve and when to install them, not building multi-step task sequences. When you’re scaling an MSP team, training time directly impacts your bottom line. A tech who takes 6 weeks to become productive with SCCM but 3 days with a modern RMM represents meaningful cost savings.
Multi-tenancy gaps
SCCM wasn’t designed for MSPs managing separate client environments. Creating proper isolation between clients requires complex configuration. Reporting across clients means building custom SQL queries or exporting data to external tools.
Purpose-built MSP platforms handle multi-tenancy from the ground up, with built-in client separation, per-client branding, and consolidated billing.
Limited cross-platform support
Most client environments include Mac, Linux, and mobile devices alongside Windows machines. SCCM handles Windows well but offers minimal support for other platforms. MSPs end up cobbling together multiple tools to manage heterogeneous environments.
Unified endpoint management platforms support Windows, macOS, Linux, iOS, and Android from a single console.
What to look for in an SCCM alternative
The best SCCM alternatives for MSPs share certain characteristics that align with how you actually deliver services.
Cloud-native architecture
Cloud platforms eliminate infrastructure management while enabling anywhere-access for distributed teams. Your techs can respond to issues from any location without VPN requirements or site-to-site connectivity. Cloud-based RMM software handles agent deployment, updates, and management automatically.
Integrated toolset
Separate tools for RMM, patching, remote access, and PSA create workflow friction. Switching between platforms slows response times and increases the chance of missed issues. Look for platforms that unify these functions. Integrated PSA and RMM platforms reduce context switching and keep all client data in one place.
Automation at scale
Manual tasks don’t scale across dozens of clients. With SCCM, automating means creating collections with membership rules, building task sequences, and configuring maintenance windows per collection. Want to patch all web servers across 30 clients during their maintenance windows? You’re creating 30+ collections with complex query rules, configuring individual deployment schedules, and maintaining this configuration as clients add or remove servers.
The right platform automates patch approvals (auto-approve Microsoft updates tested by vendors), routine maintenance (clear temp files, restart services, check disk space), monitoring thresholds (adjusted based on device role and client SLAs), and reporting (generated automatically and emailed to clients) without per-client configuration. Automated patch management sets policies once at the template level, applies to new clients in seconds. When a compliance requirement changes, update the template and all clients inherit the change.
Real-time visibility
SCCM’s inventory updates on schedules you define, creating visibility gaps. Modern remote monitoring platforms provide real-time device status, immediate alerting, and current patch compliance across all clients.
| Feature | SCCM | Cloud-based MSP platforms |
| Infrastructure required | Dedicated servers, SQL, and distribution points per site | None (agent-based, cloud console) |
| Initial setup time | 2-4 weeks per deployment | 1-3 days |
| Tech training time | 4-6 weeks | 2-5 days |
| Multi-tenant architecture | Complex workarounds needed | Built-in client separation |
| Cross-platform support | Windows only (limited Mac/Linux) | Windows, macOS, Linux, iOS, Android |
| Patch automation | Collection-based, manual configuration | Template-based policies, auto-inheritance |
| Remote access | VPN or site-to-site required | Direct internet connection |
| PSA integration | Custom development | Native integrations |
| Pricing model | Enterprise licensing (bundled, hidden costs) | Per-endpoint ($4-8/month) |
| Maintenance overhead | High (patch the patcher, SQL management) | Minimal (vendor-managed) |
| Scalability | Linear infrastructure growth | Scale without adding servers |
Top SCCM alternatives for MSPs
These platforms address SCCM’s limitations while adding MSP-specific capabilities.
Cloud-based RMM platforms
NinjaOne ranks #1 in RMM on G2 with Windows, Mac, and Linux support. The platform combines monitoring, patching, remote access, and backup in one interface. Teams report 93% less time spent on patching compared to manual processes.
Atera offers a per-technician pricing model that includes unlimited endpoints, making it attractive for MSPs managing large client bases. The platform includes PSA capabilities alongside RMM functions, though some users report the interface feels cluttered.
Datto RMM (now Kaseya) integrates tightly with Datto’s backup and business continuity solutions. Teams already using Datto hardware benefit from the unified platform, though the acquisition by Kaseya has created uncertainty about future development.
Specialized patching tools
Automox focuses exclusively on patch management across Windows, macOS, and Linux. The cloud-native platform automates patch testing, approval workflows, and deployment schedules. Organizations using other tools for monitoring and remote access sometimes add Automox specifically for patching.
Action1 delivers real-time vulnerability scanning and patch deployment without requiring on-premise servers. The platform targets teams that need Windows patching without the broader RMM feature set.
Unified endpoint management
Microsoft’s Intune represents Microsoft’s own cloud-based answer to SCCM. For organizations committed to the Microsoft ecosystem, Intune offers familiar concepts with cloud delivery. The platform integrates with Microsoft 365 and Azure Active Directory but lacks features MSPs need for client management and billing.
ManageEngine Desktop Central provides on-premise and cloud deployment options. The platform handles patch management, software deployment, and remote control for Windows, Mac, and Linux. Some MSPs appreciate the flexibility to keep client data on-premise when required.
Making the switch: migration considerations
Moving from SCCM to a new platform requires planning, but the process is less disruptive than many teams expect.
Inventory and assessment
Start by documenting what SCCM currently manages. List all managed devices, deployed applications, custom task sequences, and reporting requirements. This inventory becomes your migration checklist.
Identify which SCCM features you actually use versus capabilities that seemed important during initial setup but never provided value. Many organizations discover they’re only using 30% of SCCM’s functions.
Pilot programs
Choose a single client site for initial deployment of your new platform. Smaller sites with fewer applications make ideal pilots, but don’t pick your simplest environment. You need enough complexity to surface real problems. A client with 25-50 endpoints, mixed Windows and Mac devices, and 10-15 standard applications provides good testing ground without overwhelming your team.
Run both systems in parallel for 30-60 days, comparing results and building team confidence. Pay attention to patch deployment success rates, not just whether patches deployed. SCCM might show 95% success, but your new platform reports 87%. Dig into the 8% difference. Often you’ll discover SCCM was silently failing on devices that weren’t checking in, while the new platform accurately reports device status.
Test critical workflows like emergency patching (a zero-day hits, how fast can you deploy?), after-hours remote access (can techs connect at 2 AM from home?), and compliance reporting (do generated reports match what compliance auditors need?). Document any gaps between your current process and the new tool’s capabilities. Some gaps matter, others don’t. Missing deep disk encryption policy enforcement might be irrelevant if you’re handling that at the firewall level anyway.
Phased rollout
After validating the pilot, create a rollout schedule organized by client size and complexity. Simple environments move first, building your team’s expertise before tackling clients with specialized requirements.
Plan for 2-4 weeks per client depending on size. Rushing migrations creates confusion and increases support tickets.
Integration and automation
The value of any SCCM alternative increases when it connects with your existing tools.
PSA integration
Synchronizing ticket systems with endpoint management reduces duplicate data entry and prevents issues from slipping through. When monitoring detects low disk space, the integration automatically creates a ticket, assigns it based on your routing rules, and includes device details, current disk usage, and trending data. Your tech doesn’t waste time gathering context; they start fixing the problem.
The integration works both ways. When a tech closes a ticket for “installed Office updates,” the system triggers a follow-up scan to verify Office is actually updated and the device rebooted. If the scan shows updates still pending, the ticket reopens with a note about incomplete resolution. This catches mistakes before clients notice them.
Track time accurately without switching tools. A tech remotes into a device from the RMM console, and the PSA automatically starts a timer against that client. End the session, and the time entry appears in the ticket, ready for billing. This accuracy adds up across dozens of techs and hundreds of monthly interventions.
Documentation platforms
Linking device information to documentation platforms creates a single source of truth about each client’s environment. When a tech opens a ticket, they immediately see relevant device history, configurations, and known issues.
Backup and disaster recovery
Patching failures sometimes require restoring to a previous state. Platforms that integrate with backup solutions enable quick recovery without switching tools or contexts.
Cost comparison: Total ownership beyond licenses
SCCM licensing hides under Microsoft’s enterprise agreements. You’re paying for Configuration Manager licenses, SQL Server, Windows Server instances, and additional management infrastructure. Factor in the labor: 2-3 weeks of training per tech at $150-200/hour for qualified trainers, ongoing server maintenance (patching the patching infrastructure takes 4-6 hours monthly per deployment), and troubleshooting infrastructure issues (boundary group problems, distribution point synchronization failures, and SQL performance degradation all eat staff time).
Don’t forget the hidden costs. When SCCM breaks at a client site, you’re flying someone on-site or paying for emergency remote support. When you lose a senior SCCM admin, finding replacement expertise takes months. These disruptions cost more than monthly service fees.
Cloud-based alternatives charge per endpoint per month, typically $4-8 depending on features. You avoid server costs, SQL licensing, and infrastructure maintenance. Most MSPs hit break-even within 12 months, then save money as client count grows.
Example for 500 endpoints across 25 clients:
- SCCM: $15K server hardware, $20K licenses, $10K SQL, $30K annual maintenance labor = $75K first year
- Cloud RMM: Per-endpoint RMMs cost $24k/year for 500 devices, whereas per-technician options like Syncro cost a fraction of that regardless of device count.
First-year savings: $27K-51K. Savings increase each year as you avoid hardware refreshes and reduce training costs for new hires.
Simplify client management with integrated tools
MSPs managing multiple clients can’t afford SCCM’s complexity tax. Modern platforms give you endpoint management without the infrastructure overhead, weeks-long training, or single-platform limitations.
The right SCCM alternative frees your team from tool management so they can focus on client value. Syncro’s unified platform combines RMM, PSA, and remote monitoring for MSPs who need everything in one place. Patch 500 endpoints across 25 clients from a single dashboard. Run scripts on Mac and Windows devices simultaneously. Generate client-specific reports without SQL queries.
Start streamlining your endpoint management today with a free Syncro trial.
Frequently Asked Questions
Plan for 3-6 months for a complete migration across all clients. The timeline breaks down to 2-4 weeks for your initial pilot with one client, 1-2 weeks per additional client during phased rollout, and buffer time for troubleshooting and policy refinement. MSPs with 20-30 clients typically complete migrations in 4-5 months. You can run SCCM and your new platform in parallel during the transition, so there’s no hard cutover date that puts clients at risk.
You won’t lose the data, but you’ll need to export what matters before decommissioning SCCM. Export compliance reports, inventory snapshots, and patch history as PDFs or CSV files for your records. Most MSPs discover they only reference historical SCCM data for audits, not daily operations. Modern platforms start fresh with current device state, then build new historical data going forward. If you need to reference old SCCM reports for compliance, keep the SQL database accessible in read-only mode for 12-24 months, then archive it.
Cloud platforms typically achieve higher success rates because they report device status more accurately. SCCM might show 95% patch success, but that percentage only includes devices that checked in recently. Offline devices, boundary group misconfigurations, and distribution point failures create silent failures SCCM doesn’t surface well. Cloud platforms report actual device status in real-time. You’ll see 87-92% success rates initially, but those numbers reflect reality. As you fix connectivity issues and tune policies, success rates climb to 95-98% across your entire fleet.
Keep SCCM running alongside your new platform during pilots and phased rollout. You’re paying for the servers anyway, so there’s no additional cost. This parallel operation lets you compare results, catch gaps in the new platform, and maintain business continuity. Once you’ve migrated all clients and confirmed the new platform handles everything you need, decommission SCCM infrastructure. Some MSPs repurpose the hardware for client projects, others sell it. The SQL Server license can be reallocated if you have other uses for it.
Agents continue enforcing existing policies and running scheduled tasks during internet outages. Patches already downloaded will install on schedule. Monitoring data queues locally and syncs when connectivity returns. What you lose during an outage is real-time visibility and the ability to deploy new tasks remotely. For most environments, this is acceptable since internet outages rarely last more than a few hours. If a client has unreliable connectivity, consider hybrid approaches like local policy caching or backup cellular connections. Cloud platforms handle brief disconnections well, but sites with frequent multi-hour outages need special consideration.
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