When people compare K3s and standard Kubernetes, the usual assumption is that "K3s is lightweight, so its networking must be simplified too." That's not actually where the real difference lies. K3s bundles Flannel, a CNI (Container Network Interface) plugin, by default, while standard Kubernetes built with kubeadm starts out with no CNI selected at all. This difference in starting point — whether something is already chosen for you, or whether you have to choose it yourself — is what drives real operational differences around NetworkPolicy enforcement and network performance. This article breaks down the default networking behavior of K3s versus standard Kubernetes, based on the official documentation of each project.
K3s and Standard Kubernetes Start From Different Networking Baselines
K3s bundles Flannel as one of its "Packaged Components," alongside CoreDNS and Traefik, and its default backend is vxlan. According to the official K3s documentation, if you want to disable Flannel and use a CNI of your choice, you start K3s with --flannel-backend=none and install whichever CNI plugin you prefer. If encryption is required, a wireguard-native backend is also available.
Standard Kubernetes built with kubeadm, on the other hand, treats "installing a Pod network add-on" as a separate, independent step from control-plane initialization in its official setup process. Both the kubeadm cluster creation guide and the kubeadm installation guide make clear that a kubeadm-built cluster depends on a Container Network Interface plugin, and that choosing and installing that CNI is left to whoever builds the cluster.
In other words, the idea that "K3s is a stripped-down, feature-poor version of Kubernetes" isn't quite accurate. K3s ships with a default choice already made for you, while standard Kubernetes leaves the choice itself up to you. That's a difference in design philosophy. Considering that managed services like GKE, EKS, and AKS typically ship with a CNI already configured, K3s's approach of "skipping the choice" sits closer to that end of the spectrum.
Flannel Does Not Enforce NetworkPolicy at All
Flannel, K3s's default CNI, has a clear and easily overlooked limitation. According to the official Flannel repository, Flannel focuses purely on network connectivity, and the flanneld binary does not natively enforce NetworkPolicy. If you try to use Flannel alone to restrict communication between Kubernetes namespaces, nothing actually gets restricted — all traffic remains allowed by default, often without anyone realizing it.
Flannel's own documentation lays out two options for organizations that need policy enforcement: deploying a Kubernetes SIGs network policy controller separately via a Helm chart, or pairing Flannel with a dedicated tool like Calico. In other words, Flannel deliberately limits its scope to "networking only," treating policy enforcement as a module you add on top if and when you need it.
This isn't a K3s-specific problem — choosing Flannel on standard Kubernetes carries the exact same constraint. What matters is recognizing that if you run K3s's default configuration as-is, NetworkPolicy-based namespace isolation is often simply not in effect. If enforcing NetworkPolicy is a security requirement, you'll need to consider switching to a policy-aware CNI such as Calico or Cilium.
How Does the VXLAN Overlay Affect Network Performance?
VXLAN, the overlay technology K3s uses, works by wrapping packets traveling between nodes in an additional header and tunneling them. The official Calico documentation compares VXLAN to IP-in-IP and notes that "VXLAN has a slightly higher per-packet overhead because the header is larger," while also adding that "unless you are running very network intensive workloads the difference is not something you would typically notice." Calico's own general guidance is to "run Calico without network overlay/encapsulation," since that "gives you the highest performance and simplest network; the packet that leaves your workload is the packet that goes on the wire."
The official Cilium documentation describes a similar tradeoff. Tunneling modes (VXLAN/Geneve) add encapsulation headers, which lowers the effective MTU available for payload, though enabling jumbo frames reduces the overhead ratio per packet. The advantage of tunneling is that "the network which connects the cluster nodes does not need to be made aware of the PodCIDRs," meaning it works regardless of the underlying network's configuration. Native routing mode, by contrast, requires that the underlying network be capable of routing PodCIDRs, but in exchange it avoids tunneling overhead entirely.
Seen this way, K3s's default configuration (Flannel/VXLAN) makes sense as a design choice that favors "lowering dependence on the surrounding network configuration" over raw throughput. Whether to prioritize operational simplicity or to drop the overlay in pursuit of maximum performance comes down to your workload's actual requirements.
When and How to Switch K3s to Calico or Cilium
Given everything above, here's a practical way to decide whether to keep K3s's default Flannel setup or switch to Calico or Cilium:
- If NetworkPolicy-based traffic control is a requirement: Flannel alone won't enforce it, so plan to add a policy-aware CNI such as Calico or Cilium
- If your underlying network can route Pod CIDRs: switching to Calico or Cilium's native routing mode lets you avoid overlay overhead entirely
- If operational simplicity and low dependence on network configuration matter most: sticking with K3s's default Flannel setup is often perfectly fine
There's an important practical caveat here, though. As the official K3s documentation notes, Flannel's backend setting is configured as a server node startup option, and it must be identical across every server in the cluster. In other words, choosing a CNI isn't something you casually tweak at runtime — it's a design decision you need to make at cluster build time.
How CNI plugins themselves are managed has also changed across Kubernetes versions. According to the official Kubernetes documentation, as of Kubernetes 1.24, kubelet-based CNI management (the cni-bin-dir and network-plugin flags) was removed, and CNI management now falls to the container runtime instead. Given these shifts, it's best to avoid the "just run K3s with the defaults and figure out CNI later" approach — map out your NetworkPolicy and performance requirements before going to production, and decide your CNI accordingly.
Conclusion
The real difference between K3s and standard Kubernetes isn't about having more or fewer features — it comes down to whether the important choice of CNI has already been made for you, or whether you have to make it yourself. K3s's default, Flannel/VXLAN, doesn't enforce NetworkPolicy and carries its own overlay-related overhead. At the same time, it keeps dependence on network configuration low and lets you spin up a minimal cluster quickly. What matters is understanding this tradeoff clearly, and deciding whether to switch to Calico or Cilium before going to production, based on your actual NetworkPolicy and performance requirements.
That said, figuring out the right CNI — and the right time to switch — isn't something an infrastructure team buried in day-to-day operations can easily do on the side. A managed K3s service like Kubo can optimize CNI selection on your behalf based on your NetworkPolicy and throughput requirements, while Kubo Cloud still keeps you on Pure Kubernetes — standard, upstream Kubernetes with no vendor lock-in. You no longer have to put up with the high cost, complexity, and lock-in that come with major managed services like EKS or AKS. Built on K3s, Kubo keeps all the capabilities of full Kubernetes while taking a decision as unglamorous but important as CNI selection off your plate — at a fraction of the cost.
Understanding where K3s and standard Kubernetes actually diverge on networking is the first step toward choosing K3s for the right reasons, rather than just because "it feels lighter." If your NetworkPolicy and performance requirements are already clear, now — before you build — is the right time to revisit your design, and you can start that conversation with Kubo through Contact Us.