Containers vs Virtual Machines: What to Choose in 2025 and Why It's Not Always Docker

If you think choosing between containers and virtual machines boils down to a simple "containers are faster, VMs are more secure" — prepare to reconsider. In 2025, the picture has become far more interesting and complex than it appears at first glance.

Debunking the Main Myth: Containers Won't Replace Virtual Machines

Let's start with this: containers and VMs solve different problems, and trying to pit them against each other is like comparing a hammer with a screwdriver. Yes, both are tools, but they serve different purposes.

Containers operate at the operating system level, sharing the host kernel among all running instances. Virtual machines emulate complete hardware, each with its own OS kernel. This fundamental difference defines everything else.

IEEE research shows that containers demonstrate equal or better performance compared to VMs in almost all tests. But the devil, as always, is in the details.

Performance: Numbers, Not Marketing

Let's look at real data from recent 2024-2025 studies:

Application startup: containers start in an average of 1.3 seconds versus several minutes for virtual machines. This isn't an exaggeration — these are measured metrics under identical workloads.

Deployment density: a server supporting 12 KVM-based virtual machines can simultaneously run up to 89 Docker containers with equivalent workloads while maintaining comparable performance characteristics. Resource utilization reaches 78% in containerized environments versus 42% in VM-based deployments.

Application performance: containerized applications show 28% higher throughput and 37% lower latency when handling identical workloads.

Sounds like an unconditional victory for containers? Hold on.

Disk operations: hypervisors often outperform containers thanks to caching mechanisms. In tests, KVM showed better performance in most disk I/O operations and TCP streaming benchmarks.

Memory overhead: VMs require an average of 120-150 MB overhead per instance regardless of workload size. Containers use only the necessary resources.

Security in 2025: Reality Hits the Overconfident

November 2025 brought the container community three critical vulnerabilities in runC — the low-level runtime used by Docker, Kubernetes, and most container solutions. CVE-2025-31133, CVE-2025-52565, and CVE-2025-52881 allow complete container escape and host system access.

What does this mean in practice? An attacker can manipulate mount paths and symbolic links to bypass runC isolation and write data to critical host /proc files, such as /proc/sysrq-trigger (triggering system crash) or /proc/sys/kernel/core_pattern (arbitrary code execution).

Researchers confirm: neither AppArmor nor SELinux can fully protect against these attacks in their complete form. The container runtime operates with sufficient privileges to write to arbitrary procfs files, which is more than enough for container escape.

Main recommendation: using rootless containers blocks most inadvertent writes, as runC runs with reduced privileges.

Virtual machines provide stronger isolation at the hardware level. The hypervisor remains a common attack point, but breaking through it is harder than escaping from a container through a vulnerability in the shared kernel.

Why It's Not Always Docker: Alternatives in 2025

Docker popularized containers, but in 2025 it's far from the only or always the best choice. Moreover, Docker is excessive for many tasks.

Podman: Daemonless Architecture

Podman's main advantage is the absence of a central daemon. Docker requires running dockerd, which operates with root privileges. This is a potential attack vector.

Podman runs containers as child processes of the calling user, using a fork-exec model. The CLI is fully Docker-compatible — just replace docker with podman in commands.

In 2025, Podman recorded zero security vulnerabilities, while Docker closed several critical holes, including CVE-2025-9074 — an SSRF-like vulnerability in Docker Desktop.

Benchmarks show that Podman containers can launch up to 50% faster thanks to eliminating daemon communication overhead.

LXC: System Containers

LXC (Linux Containers) provides OS-level virtualization and works differently than Docker or Podman. These are system containers that behave like lightweight virtual machines.

An LXC container runs a full init process, you can install any software, launch multiple services. Docker/Podman focus on running a single process in an ephemeral environment.

LXC is ideal when you need to:

• Migrate legacy applications expecting a traditional OS environment
• Run multiple long-lived services in one container
• Get VM-like control with lower overhead

Research shows that LXC provides performance close to bare-metal for system containers, with minimal overhead.

containerd and CRI-O: For Kubernetes

containerd is a high-level container runtime that Docker uses under the hood. It can be installed separately along with the nerdctl CLI client, which is fully Docker-compatible.

containerd is the industry standard, maintained by the Cloud Native Computing Foundation. It's the default runtime for Kubernetes.

CRI-O is designed specifically for Kubernetes from scratch. A simplified architecture reduces potential failure points and eases maintenance. Ideal for cloud-native environments where resource efficiency is critical.

When to Choose Containers

Microservices architecture: Kubernetes in 2025 manages microservices in 76% of organizations. Automation of deployment, scaling, and monitoring makes each service independent.

CI/CD pipelines: Fast startup and environment consistency are critical for continuous integration. Containers provide identical environments from development to production.

High deployment density: When you need to squeeze the maximum from hardware. Containers allow running many times more isolated environments on the same server.

Development and testing: Spin up a local environment in seconds, guarantee that "works on my machine" = "works in production."

Stateless applications: Ephemeral workloads that can be stopped and recreated without consequences — the ideal case for containers.

When to Choose Virtual Machines

Strict isolation and security: When you need complete isolation at the hardware level. Multi-tenant environments, sensitive data processing, compliance requirements.

Legacy applications: Applications requiring specific kernel versions, drivers, or simply not designed for containerization.

Heterogeneous OS: Need to run Windows applications alongside Linux? VMs are the only option.

Stateful applications with complex configuration: Databases requiring direct disk access, specific kernel configuration, long-lived processes with state preservation.

Long-term environments: When you need a stable OS that will live for months/years without recreation.

Hybrid Approach: Containers Inside VMs

Recent 2024 research showed an interesting picture: containers running on top of VMs perform slower than standalone containers, but faster than just VMs.

This approach provides:

• Isolation at the hypervisor level
• Flexibility and efficiency of containers
• An additional security layer

Kubernetes clusters are often deployed this way: worker nodes are VMs, inside which containers run. A compromise between security and performance.

Orchestration: Not Just Kubernetes

Yes, Kubernetes is the industry standard. 75% of organizations run K8s clusters in production. But that doesn't mean it suits everyone.

Docker Swarm — Docker's built-in orchestrator. Simpler to set up and manage, but less flexible. Ideal for small deployments or teams with simple requirements.

Nomad by HashiCorp — supports both containerized and non-containerized workloads. Focus on simplicity and multi-datacenter compatibility. Excellent integration with Consul, Vault, Terraform.

OpenShift — a Kubernetes overlay from Red Hat. Adds developer tooling, built-in security, enterprise support. Kubernetes under the hood, but with pre-installed integrations and guardrails.

According to DZone, top 3 use cases for Kubernetes in 2025: hybrid/multi-cloud (54%), new cloud-native apps (49%), modernizing existing apps (46%).

Practical Recommendations for 2025

1. For new projects emphasizing security: Podman with rootless mode. Daemonless architecture reduces attack surface.
2. For enterprise with compliance requirements: VMs or containers inside VMs with additional isolation. Consider Kata Containers for hypervisor-level isolation.
3. For Kubernetes clusters: containerd or CRI-O instead of full Docker. Less overhead, native integration.
4. For legacy migration: LXC as an intermediate step. System containers provide VM-like environment with lower overhead.
5. For small teams: Docker or Podman with Docker Swarm for orchestration. Don't overcomplicate infrastructure unnecessarily.

Current Security Measures

After November's runC vulnerabilities, it's critical to:

• Update runC to versions 1.2.8, 1.3.3, 1.4.0-rc.3 or newer
• Use rootless containers where possible — runC runs as an unprivileged process
• Enable user namespaces without mapping the host's root user
• Don't run untrusted images from unknown sources
• Monitor suspicious activity with symlinks during container startup
• Apply the principle of least privilege — drop unnecessary Linux capabilities
• Use read-only root filesystems and no-new-privileges flags

Conclusion: Choice Depends on the Task

Containers won't replace virtual machines, and that's normal. Each technology has its niche, its strengths.

Containers provide unmatched deployment density, deployment speed, resource efficiency. They're ideal for cloud-native applications, microservices, CI/CD.

Virtual machines offer reliable isolation, heterogeneous OS support, legacy system compatibility. They're irreplaceable where security is critical or complete hardware emulation is needed.

Docker popularized containers, but in 2025 the ecosystem is much broader. Podman offers better security through daemonless architecture. LXC fills the system container niche. containerd and CRI-O are optimized for Kubernetes.

The right choice isn't "containers or VMs," but understanding what problem you're solving and your priorities: security, performance, ease of management, compatibility.

And remember: the fastest technology is useless if it doesn't solve your problem. The most secure one too, if your team can't properly configure and maintain it.