Onboarding a New MSP in a NonProfit: What to Expect in the First 90 DaysTL;DR:
Switching to a new Managed Service Provider (MSP) is one of the most important operational decisions your NonProfit can make—especially if you’re trying to scale services across Southern New England. A solid onboarding process protects mission continuity, stabilizes your tech, reduces chaos, and positions your team to work faster and more securely. Here’s what the first 90 days should look like:
- Weeks 1–4: Deep discovery, audits, documentation, and immediate risk mitigation
- Weeks 5–8: Migration, modernization, system cleanup, and staff/volunteer training
- Weeks 9–12: Optimization, reporting, planning, and long-term strategy alignment
- Plus: Common NonProfit pitfalls to avoid

Why Onboarding Matters for Mission Continuity

For NonProfits across Southern New England, your mission doesn’t slow down just because your technology isn’t cooperating. Whether you serve families, housing programs, youth, healthcare, or human services, tech disruptions create real-world consequences: delayed intake, missed appointments, compliance gaps, frustrated staff, and lost donor confidence.

That’s why onboarding a new MSP is more than a technical transition—it’s a mission-critical stabilization period.

The onboarding process introduces order, clarity, security, and accountability so your team can serve your community without friction. The first 90 days set the tone for everything that follows.

Phase 1 (Weeks 1–4): Audit & Discovery

1. Full IT Systems Assessment

This includes:

  • Network mapping
  • Hardware/software inventory
  • Cybersecurity and compliance review
  • Backup testing
  • Internet, phone, and vendor contract evaluation
  • SaaS and Shadow IT review

Most NonProfits underestimate how much unnecessary spending or risk is hidden inside old systems, unused tools, or forgotten subscriptions. This audit brings it all to the surface.

2. Immediate Risk Mitigation

Your MSP should neutralize high-risk vulnerabilities such as: non-functioning (or unvalidated) backups, unsupported operating systems, expired security tools, Weak password and MFA enforcement and unsecured remote access

This is especially vital for NonProfits handling client data, health information, or state-funded reporting.

3. Documentation Delivered to You

A responsible MSP builds the foundation by documenting all essential technical and administrative details, including admin credentials (securely stored), network diagrams, inventory and user lists, vendor information, the current security posture, and any priority gaps that need immediate attention

For many NonProfits, onboarding is the first time leadership gains true visibility into their IT environment.

Phase 2 (Weeks 5–8): Migration, Implementation & Training

1. System Upgrades & Migrations

This may include:

  • Moving to or optimizing Microsoft 365 or Google Workspace
  • Email and security hardening
  • Migrating file servers to SharePoint/OneDrive/Vault/Drive
  • Replacing outdated hardware
  • Cleaning up permissions and old accounts
  • Implementing advanced cybersecurity layers

This is where your team starts to feel the improvements.

2. Staff & Volunteer Training

NonProfits often have varied digital literacy levels. Training should be accessible and tailored to:

  • Full-time staff
  • Remote workers
  • Program teams
  • Volunteers
  • Leadership
  • Finance/compliance personnel

Training typically includes:

  • Cybersecurity basics
  • Phishing prevention
  • How to use the help desk
  • Microsoft 365 or Google Workspace tools
  • Password and MFA best practices

3. Help Desk Integration

By this point, your team should clearly know how to submit tickets, what response times to expect, how the after-hours process works, how issues are escalated, and which services are included versus billable.

Phase 3 (Weeks 9–12): Optimization, Reporting & Strategic Planning

1. Performance Optimization

Your MSP fine-tunes performance by reviewing:
- Ticket trends
- Bandwidth usage
- Slowness root causes
- Permissions cleanup
- Endpoint performance

2. Reporting & KPI Review

You should also receive detailed reporting that summarizes the health and stability of your environment, including patch compliance, backup success rates, security incidents blocked, ticket volumes, user satisfaction trends, and opportunities to reduce licensing or SaaS waste. This reporting gives leadership clear visibility into performance, risks, and areas where improved efficiency can support mission delivery.

3. Quarterly Technology Strategy

A strong MSP helps steer long-term success. By the end of 90 days, you should have:
- A 12-month IT roadmap (that aligns with your strategic plan)
- Budget projections
- Hardware lifecycle plans
- Cybersecurity maturity goals
- Cloud migration strategy
- Grant/donor-aligned technology recommendations

Pitfalls to Avoid (NonProfit-Specific Examples)

  • Some providers slow down handoff. Avoid this by letting your new MSP lead the transition.
  • Staff may assume the worst or resist training. Clear communication prevents this.
  • Keeping outdated systems “because we’re used to them”. Legacy tools often cost more over time and introduce security risk.
  • Volunteers often access sensitive information and must follow security protocols.
  • Letting program managers use “shadow IT”. Unapproved apps and tools create data silos, compliance issues, and hidden costs.
  • Underestimating the power of a strategic roadmap. NonProfit IT should be proactive, not reactive.

Smooth Transitions Equal Better Mission Impact

A successful MSP onboarding isn’t just a technical milestone—it’s a turning point for your organization.

In the first 90 days, you should expect:
- Stronger security
- Fewer disruptions
- Faster support
- Better staff experience
- Reduced waste in IT spending
- Better visibility and reporting
- A strategic roadmap
- A partner that supports your mission at the pace you need

If your NonProfit is preparing for growth or simply needs support aligned with your mission, a smooth onboarding process creates lasting impact.

If you’d like fresh eyes on your current IT environment, request a FREE IT Systems & Risk Assessment—an easy way to uncover inefficiencies, hidden risks, and opportunities to better support your mission.