diff --git a/crates/auto_update/src/auto_update.rs b/crates/auto_update/src/auto_update.rs
index 871d053a58..cc7fd0a2b7 100644
--- a/crates/auto_update/src/auto_update.rs
+++ b/crates/auto_update/src/auto_update.rs
@@ -23,7 +23,10 @@ use smol::{fs::File, process::Command};
 use http::{HttpClient, HttpClientWithUrl};
 use release_channel::{AppCommitSha, AppVersion, ReleaseChannel};
 use std::{
-    env::consts::{ARCH, OS},
+    env::{
+        self,
+        consts::{ARCH, OS},
+    },
     ffi::OsString,
     path::PathBuf,
     sync::Arc,
@@ -138,20 +141,24 @@ pub fn init(http_client: Arc<HttpClientWithUrl>, cx: &mut AppContext) {
     let auto_updater = cx.new_model(|cx| {
         let updater = AutoUpdater::new(version, http_client);
 
-        let mut update_subscription = AutoUpdateSetting::get_global(cx)
-            .0
-            .then(|| updater.start_polling(cx));
+        if option_env!("ZED_UPDATE_EXPLANATION").is_none()
+            && env::var("ZED_UPDATE_EXPLANATION").is_err()
+        {
+            let mut update_subscription = AutoUpdateSetting::get_global(cx)
+                .0
+                .then(|| updater.start_polling(cx));
 
-        cx.observe_global::<SettingsStore>(move |updater, cx| {
-            if AutoUpdateSetting::get_global(cx).0 {
-                if update_subscription.is_none() {
-                    update_subscription = Some(updater.start_polling(cx))
+            cx.observe_global::<SettingsStore>(move |updater, cx| {
+                if AutoUpdateSetting::get_global(cx).0 {
+                    if update_subscription.is_none() {
+                        update_subscription = Some(updater.start_polling(cx))
+                    }
+                } else {
+                    update_subscription.take();
                 }
-            } else {
-                update_subscription.take();
-            }
-        })
-        .detach();
+            })
+            .detach();
+        }
 
         updater
     });
@@ -159,6 +166,26 @@ pub fn init(http_client: Arc<HttpClientWithUrl>, cx: &mut AppContext) {
 }
 
 pub fn check(_: &Check, cx: &mut WindowContext) {
+    if let Some(message) = option_env!("ZED_UPDATE_EXPLANATION") {
+        drop(cx.prompt(
+            gpui::PromptLevel::Info,
+            "Zed was installed via a package manager.",
+            Some(message),
+            &["Ok"],
+        ));
+        return;
+    }
+
+    if let Some(message) = env::var("ZED_UPDATE_EXPLANATION").ok() {
+        drop(cx.prompt(
+            gpui::PromptLevel::Info,
+            "Zed was installed via a package manager.",
+            Some(&message),
+            &["Ok"],
+        ));
+        return;
+    }
+
     if let Some(updater) = AutoUpdater::get(cx) {
         updater.update(cx, |updater, cx| updater.poll(cx));
     } else {
@@ -342,16 +369,6 @@ impl AutoUpdater {
     }
 
     async fn update(this: Model<Self>, mut cx: AsyncAppContext) -> Result<()> {
-        // Skip auto-update for flatpaks
-        #[cfg(target_os = "linux")]
-        if matches!(std::env::var("ZED_IS_FLATPAK_INSTALL"), Ok(_)) {
-            this.update(&mut cx, |this, cx| {
-                this.status = AutoUpdateStatus::Idle;
-                cx.notify();
-            })?;
-            return Ok(());
-        }
-
         let (client, current_version) = this.read_with(&cx, |this, _| {
             (this.http_client.clone(), this.current_version)
         })?;
@@ -509,7 +526,7 @@ async fn install_release_linux(
     cx: &AsyncAppContext,
 ) -> Result<()> {
     let channel = cx.update(|cx| ReleaseChannel::global(cx).dev_name())?;
-    let home_dir = PathBuf::from(std::env::var("HOME").context("no HOME env var set")?);
+    let home_dir = PathBuf::from(env::var("HOME").context("no HOME env var set")?);
 
     let extracted = temp_dir.path().join("zed");
     fs::create_dir_all(&extracted)
diff --git a/crates/cli/src/main.rs b/crates/cli/src/main.rs
index 5ab9b2029b..4132be300b 100644
--- a/crates/cli/src/main.rs
+++ b/crates/cli/src/main.rs
@@ -314,7 +314,7 @@ mod flatpak {
         if let Some(flatpak_dir) = get_flatpak_dir() {
             let mut args = vec!["/usr/bin/flatpak-spawn".into(), "--host".into()];
             args.append(&mut get_xdg_env_args());
-            args.push("--env=ZED_IS_FLATPAK_INSTALL=1".into());
+            args.push("--env=ZED_UPDATE_EXPLANATION=Please use flatpak to update zed".into());
             args.push(
                 format!(
                     "--env={EXTRA_LIB_ENV_NAME}={}",
@@ -347,7 +347,7 @@ mod flatpak {
         {
             if args.zed.is_none() {
                 args.zed = Some("/app/libexec/zed-editor".into());
-                env::set_var("ZED_IS_FLATPAK_INSTALL", "1");
+                env::set_var("ZED_UPDATE_EXPLANATION", "Please use flatpak to update zed");
             }
         }
         args
diff --git a/docs/src/development/linux.md b/docs/src/development/linux.md
index a46e872936..e83225fe92 100644
--- a/docs/src/development/linux.md
+++ b/docs/src/development/linux.md
@@ -83,6 +83,7 @@ Zed has two main binaries:
 * If you are going to provide a `.desktop` file you can find a template in `crates/zed/resources/zed.desktop.in`, and use `envsubst` to populate it with the values required.
 * You will need to ensure that the necessary libraries are installed. You can get the current list by [inspecting the built binary](https://github.com/zed-industries/zed/blob/059a4141b756cf4afac4c977afc488539aec6470/script/bundle-linux#L65-L70) on your system.
 * For an example of a complete build script, see [script/bundle-linux](https://github.com/zed-industries/zed/blob/main/script/bundle-linux).
+* You can disable Zed's auto updates and provide instructions for users who try to Update zed manually by building (or running) Zed with the environment variable `ZED_UPDATE_EXPLANATION`. For example: `ZED_UPDATE_EXPLANATION="Please use flatpak to update zed."`.
 
 ### Other things to note
 
@@ -92,7 +93,6 @@ However, we realize that many distros have other priorities. We want to work wit
 
 * Zed is a fast moving early-phase project. We typically release 2-3 builds a week to fix user-reported issues and release major features.
 * There are a couple of other `zed` binaries that may be present on linux systems ([1](https://openzfs.github.io/openzfs-docs/man/v2.2/8/zed.8.html), [2](https://zed.brimdata.io/docs/commands/zed)).
-* We automatically install updates to Zed by default (though we do need a way for [package managers to opt out](https://github.com/zed-industries/zed/issues/12588)).
 * Zed automatically installs the correct version of common developer tools in the same way as rustup/rbenv/pyenv, etc. We understand that this is contentious, [see here](https://github.com/zed-industries/zed/issues/12589).
 * We allow users to install extensions on their own and from [zed-industries/extensions](https://github.com/zed-industries/extensions). These extensions may install further tooling as needed, such as language servers. In the long run we would like to make this safer, [see here](https://github.com/zed-industries/zed/issues/12358).
 * Zed connects to a number of online services by default (AI, telemetry, collaboration). AI and our telemetry can be disabled by your users with their own zed settings or by patching our [default settings file](https://github.com/zed-industries/zed/blob/main/assets/settings/default.json).