ECS vs. EKS vs. Fargate: Which Container Orchestration for Your Startup?

You’ve containerised your application with Docker. Now you need to run those containers in production on AWS. The three main options are ECS (Elastic Container Service), EKS (Elastic Kubernetes Service), and Fargate (serverless containers).

Every AWS comparison page says “it depends on your use case.” But that doesn’t help when you need to make a decision this week and ship to production.

This guide is based on deploying containers for dozens of startups across all three platforms. We’ll cover the real costs, hidden complexity, operational overhead, and most importantly—which option makes sense for your specific situation.

The Quick Answer (If You’re In a Hurry)

Choose ECS with EC2 if:

• You want the lowest cost (but with operational overhead)
• Your team knows AWS but not Kubernetes
• You’re running steady workloads (predictable traffic)
• You’re okay managing EC2 instances
• Budget is tight ($100-300/month for small apps)

Choose ECS with Fargate if:

• You want simple container orchestration without managing servers
• You’re okay paying 30-50% more for less operational overhead
• Your traffic is variable or spiky
• You want to ship fast and iterate
• This is our recommendation for most startups

Choose EKS with EC2 if:

• Your team already knows Kubernetes
• You need Kubernetes-specific features (StatefulSets, CRDs, Operators)
• You plan to be multi-cloud eventually
• You have DevOps resources to manage Kubernetes
• Budget allows for $200-500/month minimum

Choose EKS with Fargate if:

• You need Kubernetes but don’t want to manage nodes
• You’re okay with Fargate limitations on Kubernetes
• Budget allows for premium pricing
• You want Kubernetes without the operational complexity

Now let’s dig into the details.

What Are ECS, EKS, and Fargate?

ECS (Elastic Container Service)

AWS’s native container orchestration service. Think of it as “Docker on AWS made easy.”

Key characteristics:

• AWS-native (designed specifically for AWS)
• Simpler than Kubernetes
• Integrates tightly with AWS services (ALB, CloudWatch, IAM, Secrets Manager)
• Can run on EC2 instances (you manage) or Fargate (serverless)

EKS (Elastic Kubernetes Service)

AWS’s managed Kubernetes service. Standard Kubernetes API, managed control plane.

Key characteristics:

• Industry-standard Kubernetes (CNCF certified)
• Portable across clouds (same configs work on GCP GKE, Azure AKS)
• Massive ecosystem of tools and operators
• More complex than ECS
• Can run on EC2 instances (you manage) or Fargate (serverless)

Fargate

Serverless compute for containers. Works with both ECS and EKS.

Key characteristics:

• No server management (AWS handles EC2 instances)
• Pay per vCPU and GB of memory used
• Auto-scaling built-in
• Higher cost per container than EC2
• Less control over underlying infrastructure

Important: Fargate is not an alternative to ECS/EKS it’s a launch type. You use “ECS with Fargate” or “EKS with Fargate.”

Cost Comparison: Real Numbers

Let’s compare costs for running a typical startup application: a Node.js API with Redis cache.

Application specs:

• 2 containers (API + worker)
• API: 1 vCPU, 2 GB RAM
• Worker: 0.5 vCPU, 1 GB RAM
• Running 24/7
• Moderate traffic (1M requests/month)

ECS with EC2 Instances

Infrastructure costs:

• 2 × t3.small instances (2 vCPU, 2 GB RAM each) for redundancy
• Application Load Balancer
• EBS storage

Monthly breakdown:

EC2 instances: 2 × $15 = $30/month
ALB: $16/month + $0.008/LCU-hour (~$8) = $24/month
EBS volumes: 2 × 20 GB × $0.10/GB = $4/month
Data transfer: ~$5/month

Total: ~$63/month

Pros:

• Lowest cost option
• Full control over instance types and sizing
• Can run multiple containers per instance (cost efficiency)

Cons:

• You manage instances (patching, updates, failures)
• Need to handle auto-scaling of instances
• Operational overhead

ECS with Fargate

Fargate pricing:

• Per vCPU-hour: $0.04048
• Per GB-hour: $0.004445

Monthly breakdown:

API container:
  1 vCPU × 730 hours × $0.04048 = $29.55
  2 GB × 730 hours × $0.004445 = $6.49
  Subtotal: $36.04

Worker container:
  0.5 vCPU × 730 hours × $0.04048 = $14.78
  1 GB × 730 hours × $0.004445 = $3.24
  Subtotal: $18.02

ALB: $24/month
Data transfer: ~$5/month

Total: ~$83/month

Cost vs. EC2: +32% more expensive

Pros:

• Zero server management
• Auto-scaling is trivial
• Pay only for what you use
• No instance failures to handle

Cons:

• More expensive than EC2
• Less control over underlying resources

EKS with EC2 Instances

Infrastructure costs:

• EKS control plane: $0.10/hour = $73/month
• 2 × t3.small worker nodes
• Application Load Balancer
• EBS storage

Monthly breakdown:

EKS control plane: $73/month
EC2 worker nodes: 2 × $15 = $30/month
ALB: $24/month
EBS volumes: 2 × 20 GB × $0.10/GB = $4/month
Data transfer: ~$5/month

Total: ~$136/month

Cost vs. ECS EC2: +116% more expensive (EKS control plane fee is significant)

Pros:

• Full Kubernetes capabilities
• Portable to other clouds
• Huge ecosystem

Cons:

• Most expensive option for small workloads
• Kubernetes complexity
• $73/month control plane fee even if you run nothing

EKS with Fargate

Monthly breakdown:

EKS control plane: $73/month
Fargate compute (same as ECS Fargate): $54/month
ALB: $24/month
Data transfer: ~$5/month

Total: ~$156/month

Cost vs. ECS Fargate: +88% more expensive

Pros:

• Kubernetes without managing nodes
• No capacity planning

Cons:

• Most expensive option
• Fargate limitations on Kubernetes (no DaemonSets, host networking, privileged containers)

Cost Comparison Summary

Monthly cost for same workload:

Option	Cost/Month	vs. Cheapest
ECS with EC2	$63	Baseline
ECS with Fargate	$83	+32%
EKS with EC2	$136	+116%
EKS with Fargate	$156	+148%

As you scale (10x traffic, 10x containers):

Option	Cost/Month	Notes
ECS with EC2	~$400	Most cost-efficient at scale
ECS with Fargate	~$650	Linear scaling
EKS with EC2	~$500	Control plane cost amortises
EKS with Fargate	~$900	Most expensive

Verdict: ECS with EC2 is cheapest. ECS with Fargate is best value (cost vs. operational overhead). EKS is expensive for small workloads but control plane cost matters less at scale.

Complexity and Learning Curve

ECS Complexity: Low to Medium

What you need to learn:

• Task Definitions (how to define containers)
• Services (how to run and scale tasks)
• Clusters (grouping of container instances or Fargate tasks)
• AWS integrations (ALB, IAM roles, CloudWatch)

Setup time:

• First deployment: 2-4 hours
• Production-ready setup: 1-2 days
• Team training: 3-5 days

Example ECS Task Definition:

{
  "family": "api-task",
  "networkMode": "awsvpc",
  "requiresCompatibilities": ["FARGATE"],
  "cpu": "1024",
  "memory": "2048",
  "containerDefinitions": [
    {
      "name": "api",
      "image": "my-api:latest",
      "portMappings": [
        {
          "containerPort": 3000,
          "protocol": "tcp"
        }
      ],
      "environment": [
        {
          "name": "NODE_ENV",
          "value": "production"
        }
      ],
      "logConfiguration": {
        "logDriver": "awslogs",
        "options": {
          "awslogs-group": "/ecs/api",
          "awslogs-region": "ap-southeast-2",
          "awslogs-stream-prefix": "ecs"
        }
      }
    }
  ]
}

Pros:

• Simple mental model (just tasks and services)
• AWS-native (feels familiar if you know AWS)
• Less to learn than Kubernetes

Cons:

• AWS-specific (not portable)
• Some concepts feel awkward (task definitions vs. services)

EKS Complexity: High

What you need to learn:

• Kubernetes core concepts (Pods, Deployments, Services, ConfigMaps, Secrets)
• Kubernetes networking (CNI, Ingress, Network Policies)
• Helm (package manager for Kubernetes)
• kubectl (command-line tool)
• AWS-specific integrations (IAM Roles for Service Accounts, ALB Ingress Controller)

Setup time:

• First deployment: 4-8 hours (if you know Kubernetes already)
• Production-ready setup: 1-2 weeks
• Team training: 2-4 weeks (if starting from zero)

Example Kubernetes Deployment:

apiVersion: apps/v1
kind: Deployment
metadata:
  name: api-deployment
spec:
  replicas: 2
  selector:
    matchLabels:
      app: api
  template:
    metadata:
      labels:
        app: api
    spec:
      containers:
      - name: api
        image: my-api:latest
        ports:
        - containerPort: 3000
        env:
        - name: NODE_ENV
          value: "production"
---
apiVersion: v1
kind: Service
metadata:
  name: api-service
spec:
  selector:
    app: api
  ports:
  - protocol: TCP
    port: 80
    targetPort: 3000
  type: LoadBalancer

Pros:

• Industry standard (skills are portable)
• Huge ecosystem and community
• Powerful features (StatefulSets, CRDs, Operators)

Cons:

• Steep learning curve
• Many concepts to master
• Easy to misconfigure and create security holes

Verdict: ECS is much simpler. EKS requires significant investment in learning Kubernetes (worth it if you need Kubernetes, overkill if you just want to run containers).

Operational Overhead

How much time will your team spend managing the platform?

ECS with EC2: Medium Overhead

Ongoing tasks:

• Patch and update EC2 instances monthly
• Monitor instance health and replace failed instances
• Scale EC2 cluster as container demand grows
• Manage ECS agent updates
• Optimise instance types and sizes

Estimated time: 5-10 hours/month for a small team

Automation helps:

• Use Auto Scaling Groups for instance management
• Use Systems Manager for patching
• Use CloudWatch alarms for monitoring

ECS with Fargate: Low Overhead

Ongoing tasks:

• Monitor task health (containers can still fail)
• Optimise task CPU/memory allocations
• Review costs and right-size containers

Estimated time: 2-3 hours/month

Why less overhead:

• No servers to manage
• No patching
• Auto-scaling is built-in

EKS with EC2: High Overhead

Ongoing tasks:

• Patch and update worker nodes
• Upgrade Kubernetes version (1-2 times/year, non-trivial)
• Manage add-ons (ALB Ingress Controller, Cluster Autoscaler, Metrics Server)
• Monitor control plane and node health
• Troubleshoot Kubernetes-specific issues
• Keep Helm charts updated

Estimated time: 10-20 hours/month for a small team

Kubernetes expertise required:

• Understanding of Kubernetes architecture
• Debugging skills (pods, events, logs)
• Security best practices (RBAC, Pod Security Policies)

EKS with Fargate: Medium Overhead

Ongoing tasks:

• Upgrade Kubernetes version (AWS handles nodes, you handle workloads)
• Manage Kubernetes add-ons
• Monitor pod health
• Troubleshoot Kubernetes-specific issues (but no node troubleshooting)

Estimated time: 5-8 hours/month

Trade-off: Still need Kubernetes knowledge, but less infrastructure management.

Verdict: ECS with Fargate has the lowest operational overhead. EKS with EC2 has the highest. Choose based on your team’s capacity and expertise.

Feature Comparison

ECS Strengths

What ECS does well:

• Tight AWS integration (IAM task roles, Secrets Manager, Parameter Store, CloudWatch)
• Service Connect (service mesh-like features without complexity)
• Blue/green deployments built-in with CodeDeploy
• Capacity providers (mix EC2 and Fargate in same service)

What ECS lacks:

• No StatefulSets (managing stateful applications is harder)
• Limited ecosystem compared to Kubernetes
• AWS-specific (can’t migrate to other clouds easily)

EKS Strengths

What EKS does well:

• Full Kubernetes API (use any Kubernetes tool or operator)
• StatefulSets, DaemonSets, Jobs, CronJobs (advanced workload types)
• Custom Resource Definitions (extend Kubernetes)
• Helm ecosystem (thousands of pre-built charts)
• Service meshes (Istio, Linkerd)
• GitOps tools (ArgoCD, Flux)

What EKS lacks:

• Complexity (more moving parts)
• AWS-specific integrations require add-ons (ALB Ingress Controller, etc.)

Verdict: ECS is simpler and AWS-native. EKS is more powerful and portable.

When You Outgrow Your Choice

Migrating from ECS to EKS

Why you might migrate:

• Need Kubernetes-specific features
• Hiring engineers who only know Kubernetes
• Planning multi-cloud strategy

Challenges:

• Complete rewrite of deployment configs (Task Definitions → Kubernetes Manifests)
• Learning Kubernetes
• 2-4 weeks of migration work for a moderate-sized application

Migrating from EKS to ECS

Why you might migrate:

• Kubernetes is overkill for your needs
• Want to reduce operational overhead
• Reduce costs

Challenges:

• Lose Kubernetes-specific features
• Rewrite Kubernetes Manifests as ECS Task Definitions
• Team needs to learn ECS

Verdict: Migrations are painful. Choose wisely upfront, or accept the migration cost when it makes sense.

Real-World Scenarios

Scenario 1: Early-Stage Startup, Simple API

Your stack:

• Node.js API
• PostgreSQL RDS
• Redis ElastiCache
• 2-3 containers

ECS with Fargate:

• Cost: ~$80/month
• Setup time: 4 hours
• Operational overhead: 2 hours/month
• Best fit ✅

ECS with EC2:

• Cost: ~$60/month
• Setup time: 6 hours
• Operational overhead: 8 hours/month
• Overkill for small app

EKS:

• Cost: ~$140+/month
• Setup time: 1-2 weeks
• Operational overhead: 10+ hours/month
• Massive overkill

Winner: ECS with Fargate (simplicity and low operational overhead worth the extra $20/month)

Scenario 2: Startup with Kubernetes-Savvy Team

Your team:

• 5 engineers, all know Kubernetes
• Previous experience at companies using Kubernetes
• Running microservices architecture (10+ services)

ECS:

• Team doesn’t know ECS
• Would need to learn AWS-specific concepts
• Limited ecosystem vs. Kubernetes

EKS:

• Team already knows Kubernetes
• Can use familiar tools (kubectl, Helm, ArgoCD)
• Leverage existing knowledge
• Best fit ✅

Winner: EKS (team expertise matters more than cost)

Scenario 3: Cost-Sensitive Startup, Predictable Traffic

Your constraints:

• Budget: $200/month max for infrastructure
• Traffic is steady (SaaS with subscription model)
• Can dedicate time to operational tasks

ECS with EC2:

• Cost: ~$100/month (3 t3.small instances)
• Can run 10+ containers on 3 instances
• Predictable cost
• Best fit ✅

ECS with Fargate:

• Cost: ~$250/month (10 small containers)
• Exceeds budget

Winner: ECS with EC2 (lowest cost for steady workloads)

Our Recommendation Framework

Choose ECS with Fargate if:

• Your team doesn’t have dedicated DevOps resources
• You want to ship fast and iterate
• Your traffic is variable or spiky
• You value simplicity over cost optimisation
• You’re okay with AWS vendor lock-in
• This is our default recommendation for most startups

Choose ECS with EC2 if:

• Budget is very tight (< $200/month for infrastructure)
• Your traffic is steady and predictable
• You can dedicate time to operational overhead
• You need maximum cost efficiency
• You’re comfortable managing EC2 instances

Choose EKS with Fargate if:

• You need Kubernetes but don’t want to manage nodes
• Your team already knows Kubernetes
• Budget allows for premium pricing (~$150+/month minimum)
• You don’t need advanced Kubernetes features (DaemonSets, host networking)

Choose EKS with EC2 if:

• Your team has strong Kubernetes expertise
• You need Kubernetes-specific features (StatefulSets, Operators, CRDs)
• You plan to be multi-cloud or hybrid cloud
• You have 10+ microservices
• You have DevOps resources to manage Kubernetes
• Budget allows for $300+/month minimum

Conclusion

For 80% of startups: Start with ECS and Fargate. It’s the best balance of simplicity, cost, and operational overhead.

If budget is extremely tight: Use ECS with EC2, but know you’re trading money for time.

If your team knows Kubernetes: Use EKS. Don’t force them to learn ECS when they’re productive with Kubernetes already.

If you don’t know either: Start with ECS. It’s simpler and you can always migrate to EKS later if you need Kubernetes-specific features.

Cost comparison for typical startup (3 containers, 24/7):

• ECS + EC2: ~$80/month (cheapest, most operational work)
• ECS + Fargate: ~$110/month (best value, our recommendation)
• EKS + EC2: ~$180/month (expensive for small workload)
• EKS + Fargate: ~$200/month (most expensive, least operational work)

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