diff --git a/changelog.d/fixes/6828-bootstrap-filter-empty-env.md b/changelog.d/fixes/6828-bootstrap-filter-empty-env.md
new file mode 100644
index 0000000000..d4a6ca34ad
--- /dev/null
+++ b/changelog.d/fixes/6828-bootstrap-filter-empty-env.md
@@ -0,0 +1 @@
+- **fix(bootstrap):** filter empty `process.env` values before spawning embedded services so a blank env var no longer crashes the Docker bootstrap in a restart loop (#6828 — thanks @AndrianBalanescu).
diff --git a/scripts/build/bootstrap-env.mjs b/scripts/build/bootstrap-env.mjs
index 90ee46ddd6..e3bdd673ec 100644
--- a/scripts/build/bootstrap-env.mjs
+++ b/scripts/build/bootstrap-env.mjs
@@ -173,7 +173,14 @@ export function bootstrapEnv({ dataDirOverride, quiet = false } = {}) {
   const preferredEnvFiltered = Object.fromEntries(
     Object.entries(preferredEnv).filter(([, v]) => typeof v === "string" && v.length > 0)
   );
-  const merged = { ...persisted, ...preferredEnvFiltered, ...process.env };
+  // Filter empty strings from process.env so that Docker `-e KEY=` (which sets an
+  // empty string) does not override real values persisted in server.env or set
+  // in .env. Only shell/Docker vars that the operator actually set should win.
+  // Mirrors the filtering already applied to preferredEnv above. (fixes #6824)
+  const processEnvFiltered = Object.fromEntries(
+    Object.entries(process.env).filter(([, v]) => typeof v === "string" && v.length > 0)
+  );
+  const merged = { ...persisted, ...preferredEnvFiltered, ...processEnvFiltered };
 
   // ── Auto-generate required secrets ────────────────────────────────────────
   let needsPersist = false;
diff --git a/tests/unit/bootstrap-env.test.ts b/tests/unit/bootstrap-env.test.ts
index 45d2911776..204ceea672 100644
--- a/tests/unit/bootstrap-env.test.ts
+++ b/tests/unit/bootstrap-env.test.ts
@@ -120,6 +120,30 @@ test("bootstrapEnv fails closed when existing database cannot be inspected", ()
   });
 });
 
+test("bootstrapEnv ignores blank process.env values that would override persisted secrets (#6824)", () => {
+  withTempEnv(({ dataDir }) => {
+    process.env.DATA_DIR = dataDir;
+    fs.mkdirSync(dataDir, { recursive: true });
+
+    // Persisted secrets in server.env
+    fs.writeFileSync(
+      path.join(dataDir, "server.env"),
+      "STORAGE_ENCRYPTION_KEY=persisted-key\nJWT_SECRET=persisted-jwt\n",
+      "utf8"
+    );
+
+    // Simulate Docker `-e STORAGE_ENCRYPTION_KEY=` — sets an empty string
+    process.env.STORAGE_ENCRYPTION_KEY = "";
+    process.env.JWT_SECRET = "";
+
+    const env = bootstrapEnv({ quiet: true });
+
+    // Empty process.env values must NOT override persisted secrets
+    assert.equal(env.STORAGE_ENCRYPTION_KEY, "persisted-key");
+    assert.equal(env.JWT_SECRET, "persisted-jwt");
+  });
+});
+
 test("bootstrapEnv ignores blank dataDirOverride values", () => {
   withTempEnv(({ dataDir }) => {
     process.env.DATA_DIR = dataDir;