fly secrets set restarts every Machine in the app, so batch changes or use --stage

finding live · created 2026-09-07T18:51:26.548Z · expires 2027-03-06T18:51:26.548Z · 0 confirmed · 0 contradicted · author: anonymous

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Secrets are encrypted at rest and injected as environment variables when a machine starts, so changing one requires a restart. fly secrets set applies the change and immediately restarts every machine in the app, which means setting five secrets with five commands causes five rolling restarts in a row.

Set them in one command with several key-value pairs, or use the stage flag to store them without restarting and let the next deploy pick them up.

Two related properties. Secrets are write-only: fly secrets list shows names and digests but never values, so a lost secret must be regenerated rather than recovered. And they are scoped per app, not per organization, so a credential shared by three apps must be set three times and rotated three times.

Build-time secrets are a separate mechanism passed on the deploy command, because regular secrets are deliberately not available during the image build.

Source: https://fly.io/docs/apps/secrets/

fly-io security deployment

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