10 Common AWS Migration Challenges & How to Fix Them

Nitin Yadav
December 22, 2025
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A SquareOps expert guide covering the biggest AWS cloud migration challenges in 2025 and practical solutions to ensure secure, cost-efficient, zero-downtime migrations.

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AWS cloud migration continues to accelerate across SaaS, FinTech, healthcare, logistics, and enterprise IT. Yet despite better tools, mature frameworks, and widespread cloud adoption, migrations remain one of the most challenging engineering projects in 2025.

Why?

Because most legacy systems were never designed for the cloud. They carry complex dependencies, monolithic architectures, outdated databases, tight coupling, manual processes, and years of technical debt. Moving such systems to AWS requires precision, deep planning, and careful execution.

Even businesses that successfully migrate often face:

Unexpected downtime
Application breakage
Performance bottlenecks
Security misconfigurations
Cost overruns
Slow cutovers
Missing observability and governance

Cloud migration is not just a technical move it’s a business transformation involving people, processes, architecture, compliance, and long-term operations. Without the right strategy, tooling, and operational readiness, migrations fail or produce poor results.

This guide covers the 10 most common AWS migration challenges and exactly how to fix them, based on best practices used by AWS, cloud architects, and enterprise SRE teams.

Before that, let’s start with a pre-migration checklist every organization must complete.

Pre-Migration Checklist (Essential for a Successful AWS Migration)

Before moving a single workload to AWS, organizations must validate their readiness. Skipping this stage is one of the biggest reasons migrations fail. Here’s a practical, AWS-aligned pre-migration checklist to ensure your migration starts on the right foundation.

1. Define Business Objectives & KPIs

Clarify why you’re migrating:

Cost reduction
Faster deployments
Scalability
Compliance
Modernization

KPIs guide your architectural decisions.

2. Map Application Dependencies

Most legacy apps have hidden dependencies.
Use: AWS Application Discovery Service, X-Ray, or manual mapping.

3. Confirm Data Migration Strategy

Choose between:

Online migration (DMS)
Offline migration (Snowball)
Hybrid phased transfers

Consider size, downtime tolerance, and security.

4. Prepare AWS Landing Zone

Set up:

Multi-account structure
VPC networking
IAM governance
Logging & monitoring
S3 + KMS + GuardDuty

This becomes your foundation.

5. Security Baseline

Enable:

IAM best practices
Encryption everywhere
Security groups & NACLs
Secrets Manager / SSM Parameter Store

6. Right-Sizing & Architecture Assessment

Don’t migrate “as is.”
Review compute, storage, networks, and databases.

7. Tooling & Automation Readiness

Prepare for:

IaC (Terraform/CloudFormation)
CI/CD pipelines
Monitoring setup

8. DR & Backup Plan

Define RPO/RTO and replication strategy before migration.

9. Compliance Requirements

Identify whether SOC2, HIPAA, PCI DSS, GDPR apply.

10. Testing & Cutover Strategy

Blue/green? Canary? Big bang?
Define it early.

This checklist prevents costly surprises and sets the stage for a smooth AWS migration.

Challenge 1: Lack of a Clear Migration Strategy

One of the biggest reasons AWS migrations fail is starting without a defined strategy. Many organizations simply “lift and shift” workloads to AWS without understanding how those workloads should operate in a cloud-native environment. This leads to performance issues, higher costs, and architecture that doesn’t scale.

Symptoms

Confusion about what to migrate first
Unexpected downtime during cutover
Overprovisioned or mis-sized infrastructure
Poor performance immediately after migration

Root Cause

Teams skip discovery and jump directly into execution. They treat cloud migration as a technical task rather than a phased transformation.

How to Fix It

Use AWS’s 6Rs Migration Framework:

Rehost (lift & shift)
Replatform (lift, tinker & shift)
Refactor (modernize + microservices)
Repurchase (SaaS replacement)
Retire (remove unused workloads)
Retain (keep certain systems on-prem)

Define the right path for each application based on complexity, ROI, and business value.

Tools to Use

AWS Migration Hub
AWS Well-Architected Tool
SquareOps migration blueprinting (optional CTA later)

A clear strategy ensures migrations are predictable, cost-efficient, and aligned with business goals.

Challenge 2: Poor Application Dependency Mapping

Most legacy applications are tightly coupled and deeply interconnected. During migration, teams often discover hidden dependencies databases, APIs, cron jobs, messaging systems, internal services – that weren’t documented. This leads to unexpected failures and delays.

Symptoms

Applications fail after migration
Services cannot communicate across environments
Databases break due to missing connections
Cutover takes longer than planned
Rollbacks become frequent

Root Cause

Lack of visibility into how applications talk to each other. Legacy systems typically evolve without proper documentation, making dependencies hard to track.

How to Fix It

Perform full dependency mapping before migrating:

Identify upstream & downstream connections
Document API calls, network flows, ports, and firewalls
Map cron jobs, scheduled tasks, and batch processes
Analyze database connections and shared resources

Use migration waves based on dependency groups instead of trying to migrate everything at once.

Tools to Use

AWS Application Discovery Service
AWS X-Ray (distributed tracing)
VPC Flow Logs
Third-party mapping tools (Dynatrace, Datadog APM)

Accurate dependency mapping prevents post-migration outages and ensures services operate as expected in AWS.

Challenge 3: Underestimating Data Migration Complexity

Data is often the hardest part of AWS cloud migration. Large databases, legacy formats, inconsistent schemas, and high transaction volumes make transferring data without downtime a major challenge.

Symptoms

Extremely slow data transfer speeds
Schema mismatches after migration
Inconsistent or corrupted data
Hours of downtime during cutover
Synchronization issues between old and new environments

Root Cause

Teams assume data migration is a simple copy-and-paste. But production systems continue generating data during the migration window, creating gaps unless handled correctly.

How to Fix It

Choose the right migration approach based on data size, type, and downtime tolerance:

1. Online Migration (Minimal downtime)

Use change data capture (CDC):

AWS DMS
Dual-write or replication strategy
Continuous sync until cutover

2. Offline Migration (Large datasets)

For petabyte-scale or offline workloads:

AWS Snowball / Snowmobile
Bulk S3 uploads + re-indexing

3. Staged or Hybrid Migration

Migrate in phases noncritical data first, then transactional systems.

Tools to Use

AWS Database Migration Service (DMS)
AWS Snow Family
AWS DataSync
Schema Conversion Tool (SCT)

Data migration is not just a technical task it’s a disciplined process requiring planning, testing, and validation.

Challenge 4: Security Misconfigurations

Security issues are one of the most common and dangerous AWS migration challenges. When companies rush to move workloads, they often replicate old security flaws or misconfigure new AWS services, creating vulnerabilities that attackers can exploit.

Symptoms

Publicly exposed S3 buckets
Over-permissive IAM roles (e.g., *:*)
Unencrypted databases or volumes
Open security groups (0.0.0.0/0)
Missing audit logs or monitoring
Failed compliance checks

Root Cause

Migrating without a security baseline. Teams focus on moving fast rather than securing resources from day one. This leads to “temporary” insecure configurations that never get fixed.

How to Fix It

Implement a security-first migration approach, including:

1. IAM Hardening

Enforce least privilege
Enable MFA & SSO
Use IAM Roles, not long-lived keys

2. Encryption Everywhere

KMS-managed keys
Encrypted EBS, RDS, S3, DynamoDB

3. Network Security

Restrictive security groups
Proper VPC segmentation
Private subnets for critical workloads

4. Continuous Monitoring

GuardDuty
Security Hub
CloudTrail + CloudWatch

Tools to Use

AWS IAM Access Analyzer
AWS Security Hub
AWS Config + CIS Benchmarks
Amazon GuardDuty

Security must be integrated into the migration not added afterward. A secure landing zone prevents breaches and ensures compliance.

Challenge 5: Network Performance & Connectivity Issues

Networking is one of the most underestimated components of an AWS migration. Poor VPC design, misconfigured routing, or unreliable connectivity between on-prem and AWS can cause latency spikes, application timeouts, and service failures.

Symptoms

Slow application performance after migration
High latency between services
Frequent connection drops
Inconsistent user experience
Failed API calls or DB connections

Root Cause

Legacy systems often expect low-latency, local network communication. Once migrated, these services may still depend on components that remain on-prem or reside in other regions.

How to Fix It

Adopt a modern, scalable networking architecture:

1. Use the Right Connectivity Method

VPN for small setups
AWS Direct Connect for stable, high-bandwidth traffic
Direct Connect + VPN failover for enterprise reliability

2. Architect VPCs Correctly

Separate public and private subnets
Use NAT Gateways for outbound access
Configure correct routing tables
Implement Transit Gateway for multi-VPC architectures

3. Reduce Cross-Region Traffic

Keep latency-sensitive workloads in the same region.

Tools to Use

VPC Reachability Analyzer
AWS Network Manager
CloudWatch VPC Flow Logs
Route 53 health checks

Proper network planning ensures applications remain fast, reliable, and resilient after migration.

Challenge 6: Wrong Instance Sizing (Over/Under Provisioning)

One of the most expensive AWS migration mistakes is lifting legacy workloads into the cloud without adjusting compute, storage, and database sizing. On-prem servers are typically oversized “just in case,” and migrating them as-is leads to unnecessary cloud costs.

Symptoms

High AWS bills immediately after migration
Idle CPU or memory utilization
Application throttling or slow performance
Frequent scaling issues
Over-reliance on manual resizing

Root Cause

Teams often replicate existing server configurations instead of using cloud-native sizing and autoscaling. AWS offers dozens of instance families and storage types, but incorrect selection leads to inefficiency.

How to Fix It

Adopt a data-driven rightsizing process:

1. Analyze Actual Resource Usage

Check CPU, memory, disk, and network needs before choosing instance types.

2. Use Cloud-Native Compute Options

EC2 Spot for non-critical workloads
Graviton-based instances for cost/performance
Auto Scaling Groups for dynamic workloads

3. Optimize Databases

Switch to:

Aurora (cost-effective & scalable)
DynamoDB for serverless workloads

Tools to Use

AWS Compute Optimizer
AWS Cost Explorer
AWS Trusted Advisor
SquareOps rightsizing automation scripts

Correct sizing reduces cloud bills by 30–50% and improves performance.

Challenge 7: Migration Downtime & Cutover Risks

Minimizing downtime is one of the hardest parts of AWS cloud migration. Whether you’re moving databases, monoliths, or tightly coupled legacy apps, even a few minutes of disruption can impact revenue, user trust, and SLAs.

Symptoms

Users experience errors during migration
Data loss or partial writes during cutover
Services go down for hours
Rollbacks take too long
Release teams hesitate to proceed

Root Cause

Many organizations attempt a “big bang” cutover- migrating everything at once. This approach is risky because it assumes all services will work perfectly on AWS immediately after migration.

How to Fix It

Use modern cutover strategies designed to minimize or eliminate downtime:

1. Blue/Green Deployments

Run the new AWS environment parallel to the old one and switch traffic only when stable.

2. Canary Releases

Gradually shift traffic for validation.

3. Phased Migration

Move workloads in waves – starting with non-critical systems.

4. Continuous Data Sync

Keep data synchronized using DMS or replication to avoid stale writes.

Tools to Use

AWS DMS (CDC sync)
Route 53 weighted routing
Application Load Balancer (canary traffic)
CloudEndure Migration

A well-executed cutover plan dramatically reduces downtime risks and ensures a smooth transition with minimal business impact.

Challenge 8: Lack of Governance & Multi-Account Strategy

Many organizations migrate to AWS using a single account or ad-hoc account structure. While this might work early on, it quickly leads to compliance issues, security risks, and operational chaos as cloud usage expands.

Symptoms

No clear separation between dev, staging, and production
Hard-to-track IAM permissions
Inconsistent tagging across resources
Cost visibility becomes impossible
Teams accidentally modify production resources
Compliance audits become painful

Root Cause

Skipping the foundational step of designing a multi-account governance model before migration. Legacy on-prem thinking often leads teams to treat AWS like traditional data centers.

How to Fix It

Adopt AWS’s Landing Zone + Control Tower model:

1. Structure Accounts by Function

Security
Logging
Networking
Dev / Staging / Prod
Team-specific or project-specific accounts

2. Apply Centralized Governance

Service Control Policies (SCPs)
Mandatory tagging
Cost allocation rules
IAM guardrails
CloudTrail + Config aggregation

3. Enforce Standardized Provisioning

All accounts should be created through an approved process or IaC templates.

Tools to Use

AWS Control Tower
AWS Organizations
IAM Identity Center
AWS Config

A proper multi-account strategy provides security, scalability, compliance, and cost visibility from day one.

Challenge 9: Cost Overruns Post-Migration

Many companies are shocked by their AWS bill within the first 30–60 days after migration. The cloud is pay-as-you-go, but without guardrails, it’s easy to overspend on compute, storage, networking, and unused resources.

Symptoms

AWS bill jumps significantly post-migration
Unused EC2 instances or EKS nodes remain running
Overprovisioned RDS or oversized EBS volumes
High S3 storage or data transfer costs
No visibility into which team is driving spend

Root Cause

Migrating “as is” from on-prem leads to inefficient infrastructure. Without FinOps or automated cost controls, cloud waste grows quickly.

How to Fix It

Implement continuous AWS cost governance:

1. Rightsize Compute & Databases

Analyze actual CPU, memory, and storage usage.

2. Automate Scaling

Enable autoscaling for EC2, EKS, and ECS workloads.

3. Optimize Storage

Use lifecycle policies, Glacier tiers, and EBS cleanup.

4. Purchase Savings Plans / RIs

Save 30–70% on long-term compute usage.

5. Set Budgets & Anomaly Alerts

Catch unexpected cost spikes early.

Tools to Use

AWS Cost Explorer
AWS Budgets
Trusted Advisor
Compute Optimizer
SquareOps FinOps automation modules

A mature FinOps model ensures that cloud costs remain predictable and aligned with business growth.

Challenge 10: Skills Gap & Operational Readiness

Even after a successful migration, many teams struggle to operate their new AWS environment effectively. Cloud-native systems require different skills, tools, and workflows compared to traditional on-prem environments.

Symptoms

Teams unsure how to manage autoscaling, EKS, or serverless
Slow incident response and limited monitoring
Frequent configuration errors
Difficulty managing IAM, networking, or IaC
Overwhelmed DevOps engineers

Root Cause

AWS environments demand expertise in:

IaC (Terraform, CloudFormation, CDK)
CI/CD pipelines
SRE/DevOps operations
Cloud-native security
Cost optimization & FinOps
Kubernetes (EKS)
Observability frameworks

Most internal teams haven’t operated infrastructure at this scale or complexity.

How to Fix It

Adopt a structured operational readiness plan:

1. Train Teams in Cloud-Native Practices

DevOps, security, FinOps, and SRE functions need clear ownership.

2. Implement IaC + Automation

Reduces human error and increases reliability.

3. Establish 24×7 Monitoring & On-Call Support

Essential for production workloads.

4. Create Playbooks & SOPs

Incident runbooks, escalation flows, DR procedures.

Tools to Use

AWS Well-Architected Tool
Terraform / CDK pipelines
Datadog, Prometheus, OpenTelemetry
PagerDuty / Opsgenie

Strong operational readiness ensures long-term success after migration not just a smooth launch.

AWS Cloud Migration Best Practices

After addressing the major challenges, organizations need a set of guiding best practices to ensure migrations are repeatable, resilient, and cloud-native. These principles help teams avoid costly mistakes and build a strong operational foundation in AWS.

1. Modernize Instead of Lifting Everything “As-Is”

Rehosting is fast, but not always efficient. Where possible:

Break monoliths into services
Move to managed databases (Aurora, DynamoDB)
Adopt serverless or container platforms

2. Use Infrastructure as Code (IaC)

Terraform or CloudFormation ensures consistent, automated provisioning critical for maintaining environments at scale.

3. Build CI/CD Pipelines Before Migration

Automated deployments reduce downtime, improve testing, and speed up validation.

4. Implement Observability Early

Monitoring, logging, and tracing should be part of the migration not an afterthought.

5. Enforce Security Baselines

Start with:

IAM least privilege
KMS encryption
GuardDuty + Security Hub
VPC segmentation

6. Run Well-Architected Reviews

Identify gaps in the 5 AWS pillars: Security, Cost, Reliability, Performance, Operational Excellence.

Following these best practices ensures migrations are predictable, secure, and optimized for long-term success.

Tools That Simplify AWS Migration

AWS offers a mature suite of migration tools that streamline discovery, data transfer, modernization, and cutover operations. Choosing the right tooling reduces risk and accelerates the migration timeline.

1. AWS Migration Hub

Provides a centralized dashboard to track progress across multiple migration tools and workloads.

2. AWS Application Discovery Service

Automatically identifies servers, applications, and dependencies crucial for planning migration waves.

3. AWS Database Migration Service (DMS)

Enables continuous replication with change data capture (CDC), minimizing downtime for database cutovers.

4. AWS Snow Family (Snowball, Snowcone, Snowmobile)

Used to migrate massive datasets when online transfer isn’t feasible.

5. CloudEndure Migration

Automates lift-and-shift migrations with continuous low-latency replication.

6. AWS DataSync

Fast, secure, automated data movement between on-prem and AWS.

7. IaC Tools (Terraform, CloudFormation, CDK)

Standardize and automate AWS infrastructure provisioning.

8. Monitoring & Observability Tools

Datadog, Prometheus, Grafana, and OpenTelemetry help validate performance pre- and post-migration.

These tools reduce the migration burden and help teams transition to AWS with confidence and operational visibility.

Why Many Migrations Fail (And How to Avoid It)

Even with strong planning, many AWS migrations fail not because of technology, but because of people, process, and strategy gaps. Understanding these failure points helps organizations avoid costly mistakes.

1. Leadership Underestimates Complexity

Migration is not “just copying servers to AWS.” It requires operational, architectural, and cultural change.
Fix: Set realistic timelines and align stakeholders early.

2. Over-Reliance on Lift-and-Shift

Organizations often migrate workloads without modernization. This results in high costs, slow performance, and poor scalability.
Fix: Apply the 6Rs framework and modernize where it makes sense.

3. No Cloud-Native Mindset

Teams continue using on-prem practices manual deployments, no autoscaling, minimal observability.
Fix: Adopt IaC, CI/CD, autoscaling, and cloud-native patterns.

4. Missing Security & Governance Controls

Post-migration environments become vulnerable due to rushed configurations.
Fix: Implement baselines (IAM, encryption, logging, SCPs) before migration.

5. Lack of Post-Migration Operational Readiness

Teams struggle after go-live due to missing skills.
Fix: Train engineers and establish SRE playbooks.

Understanding these pitfalls ensures your AWS migration becomes a long-term success not a costly migration failure story.

Why Companies Choose SquareOps for AWS Cloud Migration

AWS migration is complex, but with the right partner, it becomes predictable, secure, and cost-efficient. SquareOps specializes in zero-downtime migration strategies, cloud-native modernization, and end-to-end support from planning to post-migration operations.

1. Migration Blueprinting & Strategy

SquareOps builds detailed migration roadmaps using:

Dependency analysis
The 6Rs framework
Cost & performance modeling
Compliance requirements (SOC2, HIPAA, PCI DSS)

2. IaC-First Cloud Foundation

All AWS environments VPCs, EKS clusters, databases, security controls are deployed using Terraform or CDK to ensure consistency, repeatability, and faster scaling.

3. Secure-by-Design Architecture

SquareOps embeds security across every layer:

IAM least privilege
Encryption everywhere
GuardDuty + Security Hub
CIS-compliant Landing Zones

4. Downtime-Minimized Cutovers

Customers benefit from:

Blue/green migrations
Continuous database sync
Staged migration waves
Automated rollback plans

5. FinOps-Driven Optimization

Post-migration, Contact SquareOps to reduce AWS costs by 30–60% through rightsizing, waste cleanup, storage tiering, and Savings Plans strategies.

SquareOps doesn’t just migrate workloads, it modernizes them for long-term success.

Frequently asked questions

Why is AWS cloud migration still difficult in 2025?

Because legacy systems have complex dependencies, technical debt, security gaps, and are not cloud-native by design.

What are the biggest AWS migration challenges?

Common challenges include downtime, data migration complexity, security misconfigurations, cost overruns, and skills gaps.

What is the most common AWS migration mistake?

Starting migration without a clear strategy or dependency mapping is the most common cause of failure.

How can downtime be minimized during AWS migration?

Using blue-green deployments, canary releases, phased migrations, and continuous data replication.

Why do AWS costs increase after migration?

Lift-and-shift migrations, overprovisioned resources, and lack of FinOps controls often cause cost overruns.

How important is security during AWS migration?

Security is critical. IAM hardening, encryption, network isolation, and continuous monitoring must be built in from day one.

What tools help simplify AWS cloud migration?

AWS Migration Hub, DMS, Application Discovery Service, Snowball, CloudEndure, and IaC tools like Terraform.

Why do companies struggle after AWS migration?

Lack of operational readiness, missing observability, and insufficient cloud-native skills slow post-migration success.

Should companies modernize during migration?

Yes. Refactoring, re-platforming, and using managed AWS services improves scalability, performance, and cost efficiency.

How does SquareOps help with AWS cloud migration?

SquareOps delivers secure, IaC-driven, low-downtime AWS migrations with post-migration optimization and 24×7 support.

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