Part 5 — From Flannel to Cilium: Why Isovalent Enterprise Becomes the Logical Next Step

Bridging Kubernetes, Cilium, and eBPF for Network Engineers

Part 5 — From Flannel to Cilium: Why Isovalent Enterprise becomes the logical next step

Over the first four posts in this Kubernetes for Network Engineers series, we explored how Kubernetes networking fundamentally changes the way packets move, how identity replaces IP as the core of security, how Hubble restores observability in a highly dynamic environment, and how eBPF rewrites the rules for load balancing and service handling. 

Each part highlighted a dimension of Kubernetes that network engineers must reinterpret through a new overlay one shaped by cloud-native architecture and kernel-level programmability rather than traditional routing paradigms.

In the first four parts of this series, we explored how Cilium and eBPF reshape Kubernetes networking from a network engineer's perspective:

Part 1 — Networking Foundations: https://www.wwt.com/blog/bridging-kubernetes-cilium-and-ebpf-to-networking-concepts-for-network-engineers

Part 2 — Security: https://www.wwt.com/blog/bridging-kubernetes-cilium-and-ebpf-to-networking-concepts-for-network-engineers-part-2-security

Part 3 — Observability: https://www.wwt.com/blog/bridging-kubernetes-cilium-and-ebpf-to-networking-concepts-for-network-engineers-part-3-observability

Part 4 — Services: https://www.wwt.com/blog/bridging-kubernetes-cilium-and-ebpf-to-networking-concepts-for-network-engineers-part-4-services

These articles established a foundation for understanding how Kubernetes traffic flows, how identity-driven security works, how Hubble unlocks cross-cluster visibility, and how eBPF-driven policy modernizes the Kubernetes service layer.

Now, in Part 5, we take the next natural step:

Why this conversation matters

For many organizations, the journey begins with a simple CNI (container network interface) like Flannel, but it often ends with a realization: managing Kubernetes at enterprise scale requires deeper visibility, stronger security guarantees, and far more integrated feature sets than Flannel was designed to provide. This article serves as a bridge from the conceptual groundwork laid in earlier parts to the real-world operational considerations that guide the shift from Flannel toward Cilium, and increasingly toward Isovalent Enterprise for Cilium.

Most Kubernetes clusters begin with a straightforward CNI: In this example, Flannel, which is easy, stable, and purpose-built for basic pod networking.  

But as you scale, the concerns covered in Parts 1–4 quickly rise to the surface:
Advanced networking needs (kube-proxy scaling limits, cross-node load balancing)

Better security enforcement (L3–L7 identity-based policy)

Rich observability (flow tracing, service dependency maps, troubleshooting)

Production-ready service management (sidecar-free mesh, mTLS, routing)

Reduction in latency from sidecars and kernel-level speeds.

Flannel simply wasn't designed for these capabilities. Cilium was.

And Isovalent Enterprise for Cilium packages all of this into a commercially supported, production-grade platform.

Why minimalist CNIs eventually become limiting

Flannel's appeal is clear: it is lightweight, reliable, and does one job exceptionally well—basic pod-to-pod connectivity. In early cluster deployments, that is often enough. Developers can reach their microservices, workloads can scale horizontally, and the network behaves predictably.

However, as clusters mature, they begin to take on workloads that demand far more from the underlying network layer:

Identity-aware, zero-trust policies that go beyond simple L3/L4 rules

Deep observability into pod-to-pod flows, DNS behavior, and service interactions

Multi-cluster topologies where identity and policy must remain consistent across environments

Service mesh capabilities like mTLS and routing, but without the cost and complexity of sidecars

High-performance, kube-proxy-free load balancing that removes iptables bottlenecks

Transparent encryption of inter-node and inter-pod traffic

Each Sidecar is another process/service  every time we add another sidecar to enable features we add latency

Flannel was never intended to provide these capabilities. Instead, organizations bolt on additional tools often one for each missing feature. Over time, clusters accumulate a sprawling list of dependencies: Calico for policy, Istio for L7 control, Prometheus for telemetry, Submariner for multi-cluster networking, Falco for runtime signals, and so on. Each solves a problem, but collectively they introduce operational overhead.

In the simplest terms: Flannel keeps networking simple, but makes the rest of the platform complex.

Cilium: The Integrated, eBPF-Powered Data Plane

Cilium fundamentally changes this dynamic by making the Linux kernel the point of integration. Through eBPF, Cilium moves networking, security, observability, and service handling into a unified dataplane that operates at kernel speed and with kernel-level insight.

The capabilities we explored in Parts 1–4 come together seamlessly here:

Networking: Cilium's eBPF-based kube-proxy replacement eliminates the performance randomness of iptables, improves scalability, and offers consistent hashing for stable load balancing.

Security: Cilium enforces policy by Kubernetes identity, not IP, enabling L3/L4/L7 enforcement that adapts dynamically to pod lifecycle changes.

Observability: Hubble provides immediate, real-time transparency into traffic patterns—with flows, service dependencies, DNS lookups, and detailed L7 metrics.

Services: Cilium's sidecar-free service mesh uses eBPF and Envoy at the right enforcement points, dramatically reducing operational cost compared to sidecar-heavy meshes.

Cilium is not simply "more features." It is a single, coherent system that naturally aligns with modern Kubernetes expectations. Instead of piecing together a stack of disparate tools, the platform team gets a unified solution delivered through the kernel itself.

Isovalent Enterprise: Taking Cilium from Feature-Rich to Production-Ready

While open-source Cilium provides all the core capabilities, enterprise environments often require more: predictable releases, long-term support, certified builds, deep auditability, and integration with SIEM and compliance frameworks. This is where Isovalent Enterprise for Cilium enters.

Isovalent builds on the open-source foundation and extends it with:

Curated, production-grade releases validated for stability

Cisco/Isovalent-backed 24×7 support

Historical flow retention for incident analysis and compliance investigations

Advanced visibility tools for operators to correlate network, identity, and process behaviors

Air-gapped and private cloud support

Runtime security insights built directly into the platform

In regulated or large-scale environments, these features move from "nice to have" to "absolutely required." Enterprises don't simply need a feature-rich dataplane—they need an operational platform that fits into existing security, audit, and monitoring frameworks. Isovalent provides this bridge.

Comparison: Flannel + Add-Ons vs. Cilium vs. Isovalent Enterprise

Even with an expanded narrative, a clear comparison remains essential. Here is the chart retained and polished for clarity:

Comparison table

Key takeaways

Stay with Flannel if:

• Small clusters
• Basic networking needs
• Minimal operations team

Choose Cilium Open Source if:

• Need advanced features without licensing
• Comfortable operating open-source
• Working to improve latency from sidecars

Choose Isovalent Enterprise if:

• Multi-cluster / multi-cloud
• Compliance and audit requirements
• Need SLAs and supported releases

Final thoughts

Your CNI defines how you enforce security, observe traffic, scale services, and operate Kubernetes at an enterprise level.

Flannel is a solid beginning. Cilium is the natural evolution. Isovalent Enterprise is the operational destination.