Traffic is spiky — scale to zero and pay only per request. You are starting a new project — Google recommends it as the default. You need GPUs, fast deploys, or percentage-based traffic splitting.

Cloud Run vs App Engine Flexible? · Decisions

The verdict

Cloud Run is Google's modern default — its own documentation recommends it over App Engine for new users, citing advanced capabilities such as GPUs at lower prices. It scales to zero and bills per request. App Engine Flexible is not deprecated and remains supported, but it is a legacy option: it still fits when you need VM-level control (Compute Engine VMs with SSH), workloads that must sit in the Compute Engine network, or steady traffic where an always-on instance is acceptable. The deciding factor is scale-to-zero and billing — Cloud Run charges nothing when idle; Flexible always keeps a billable VM running.

Head to head

Criterion	Cloud Run	App Engine Flexible
Scale to zero	Yes — idle revisions scale to 0 instances	No — at least one instance always runs
Billing when idle	Request-based billing — no charge when idle	Instances billed continuously
Deploy unit	Any OCI / Docker container, as an immutable revision	A Docker container on Compute Engine VMs
Cold starts	Yes — scale-from-zero	None — no scale-from-zero
Startup speed	Seconds	Minutes — VM boot
Request timeout	Default 5 min, configurable to 60 min	60 min
GPU support	Yes — NVIDIA L4 and RTX PRO 6000	No
VM-level access	No host access	Yes — SSH into the underlying Compute Engine VM
Positioning	Modern, recommended default for new projects	Supported; Cloud Run recommended instead

When to pick which

Pick Cloud Run when

Traffic is spiky — scale to zero and pay only per request.
You are starting a new project — Google recommends it as the default.
You need GPUs, fast deploys, or percentage-based traffic splitting.

Pick App Engine Flexible when

You need VM-level control — SSH into the Compute Engine VM for debugging.
Your app must run inside the Compute Engine network.
You have an existing Flexible app and migration cost outweighs modernising now.

Sources

Compare App Engine and Cloud Run — https://docs.cloud.google.com/appengine/migration-center/run/compare-gae-with-run
Cloud Run instance autoscaling — https://docs.cloud.google.com/run/docs/about-instance-autoscaling
Cloud Run billing settings — https://docs.cloud.google.com/run/docs/configuring/billing-settings
Cloud Run request timeout — https://docs.cloud.google.com/run/docs/configuring/request-timeout
Cloud Run GPU configuration — https://docs.cloud.google.com/run/docs/configuring/services/gpu
App Engine flexible environment overview — https://docs.cloud.google.com/appengine/docs/flexible/overview

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