diff --git a/src/Lean/Elab/Attributes.lean b/src/Lean/Elab/Attributes.lean
index dae6c6fc3e2e..fe3fd8eae882 100644
--- a/src/Lean/Elab/Attributes.lean
+++ b/src/Lean/Elab/Attributes.lean
@@ -63,6 +63,16 @@ def elabAttr [Monad m] [MonadEnv m] [MonadResolveName m] [MonadError m] [MonadMa
       | throwError "Unknown attribute `[{attrName}]`"
     if let .ok impl := getAttributeImpl (← getEnv) attrName then
       if regularInitAttr.getParam? (← getEnv) impl.ref |>.isSome then  -- skip `builtin_initialize` attributes
+        -- Reject attribute uses where the implementation's home module has been loaded for IR only:
+        -- in that case `metaExt` is missing and shake's `recordExtraModUseFromDecl` would record a
+        -- stale `isMeta` flag (issue #13599). Force the user to import the module as a regular dep.
+        if let some idx := (← getEnv).getModuleIdxFor? impl.ref then
+          let env ← getEnv
+          if env.header.modules[idx]?.any (!·.hasData) then
+            let modName := env.header.modules[idx]!.module
+            throwError m!"Cannot use attribute `[{attrName}]`: module `{modName}` is loaded for IR \
+              only (reached as a private `meta` dependency). Add a non-private import \
+              of `{modName}`."
         recordExtraModUseFromDecl (isMeta := true) impl.ref
     /- The `AttrM` does not have sufficient information for expanding macros in `args`.
       So, we expand them before here before we invoke the attributer handlers implemented using `AttrM`. -/
diff --git a/src/Lean/Environment.lean b/src/Lean/Environment.lean
index 9bd043e8ff97..7b5721899bc2 100644
--- a/src/Lean/Environment.lean
+++ b/src/Lean/Environment.lean
@@ -147,6 +147,8 @@ structure ModuleData where
 structure EffectiveImport extends Import where
   /-- Phases for which the import's IR is available. -/
   irPhases : IRPhases
+  /-- Whether the import's `.olean*` data has been loaded (otherwise only the `.ir` is). -/
+  hasData : Bool
 deriving Inhabited
 
 /-- Environment fields that are not used often. -/
@@ -1980,14 +1982,12 @@ private structure ImportedModule extends EffectiveImport where
   parts     : Array (ModuleData × CompactedRegion)
   /-- `.ir` data, if loaded. -/
   irData?   : Option (ModuleData × CompactedRegion)
-  /-- If true, `.olean*` data should be imported. -/
-  needsData : Bool
   /-- If true, IR is loaded transitively. -/
   needsIRTrans : Bool
 
 /-- The main module data that will eventually be used to construct the publicly accessible constants. -/
 private def ImportedModule.publicModule? (self : ImportedModule) : Option ModuleData := do
-  if self.needsData then
+  if self.hasData then
     self.parts[0]?.map (·.1)
   else
     -- (should not have any constants)
@@ -2000,7 +2000,7 @@ private def ImportedModule.getData? (self : ImportedModule) (level : OLeanLevel)
 
 /-- The main module data that will eventually be used to construct the kernel environment. -/
 private def ImportedModule.mainModule? (self : ImportedModule) : Option ModuleData :=
-  if self.needsData then
+  if self.hasData then
     self.getData? (if self.importAll then .private else .exported)
   else
     self.irData?.map (·.1)
@@ -2150,16 +2150,16 @@ where
         -- when module is already imported, bump flags
         let importAll := importAll || mod.importAll
         let isExported := isExported || mod.isExported
-        let needsData := needsData || mod.needsData
+        let needsData := needsData || mod.hasData
         let needsIRTrans := needsIRTrans || mod.needsIRTrans
         let needsIR := needsIRTrans || importAll
         let irPhases := if irPhases == mod.irPhases then irPhases else .all
         let parts ← if needsData && mod.parts.isEmpty then loadData i else pure mod.parts
         let irData? ← if needsIR && mod.irData?.isNone then loadIR? i else pure mod.irData?
         if importAll != mod.importAll || isExported != mod.isExported ||
-            needsIRTrans != mod.needsIRTrans || needsData != mod.needsData || irPhases != mod.irPhases then
+            needsIRTrans != mod.needsIRTrans || needsData != mod.hasData || irPhases != mod.irPhases then
           modify fun s => { s with moduleNameMap := s.moduleNameMap.insert i.module { mod with
-            importAll, isExported, irPhases, parts, irData?, needsData, needsIRTrans }}
+            importAll, isExported, irPhases, parts, irData?, hasData := needsData, needsIRTrans }}
           -- bump entire closure
           goRec mod
         continue
@@ -2167,7 +2167,7 @@ where
       -- newly discovered module
       let parts ← if needsData then loadData i else pure #[]
       let irData? ← if needsIR then loadIR? i else pure none
-      let mod := { i with importAll, isExported, irPhases, parts, irData?, needsIRTrans, needsData }
+      let mod := { i with importAll, isExported, irPhases, parts, irData?, needsIRTrans, hasData := needsData }
       goRec mod
       modify fun s => { s with
         moduleNameMap := s.moduleNameMap.insert i.module mod
diff --git a/tests/pkg/user_attr/UserAttr.lean b/tests/pkg/user_attr/UserAttr.lean
index ec633fea1cf1..24e108990f72 100644
--- a/tests/pkg/user_attr/UserAttr.lean
+++ b/tests/pkg/user_attr/UserAttr.lean
@@ -1,4 +1,5 @@
 import UserAttr.Tst
+import UserAttr.MetaUser
 
 open Lean
 
diff --git a/tests/pkg/user_attr/UserAttr/MetaMid.lean b/tests/pkg/user_attr/UserAttr/MetaMid.lean
new file mode 100644
index 000000000000..fd8303405fbc
--- /dev/null
+++ b/tests/pkg/user_attr/UserAttr/MetaMid.lean
@@ -0,0 +1,13 @@
+module
+
+import UserAttr.BlaAttr
+
+/-! Middle module that plain-imports `UserAttr.BlaAttr`, used by `UserAttr.MetaUser` to set up the
+`meta import` chain that triggers the regression in
+https://github.com/leanprover/lean4/issues/13599. -/
+
+@[expose] public section
+
+def midVal : Nat := 17
+
+end
diff --git a/tests/pkg/user_attr/UserAttr/MetaUser.lean b/tests/pkg/user_attr/UserAttr/MetaUser.lean
new file mode 100644
index 000000000000..acb9760014a7
--- /dev/null
+++ b/tests/pkg/user_attr/UserAttr/MetaUser.lean
@@ -0,0 +1,20 @@
+module
+
+public meta import UserAttr.MetaMid
+meta import Lean.Elab.GuardMsgs
+
+/-! Regression test for https://github.com/leanprover/lean4/issues/13599: using `@[my_simp]` (an
+attribute registered in `UserAttr.BlaAttr`) while reaching `BlaAttr` only via a `meta import`
+chain (`UserAttr.MetaMid → import UserAttr.BlaAttr`) used to make `shake --fix` flip-flop. The
+elaborator now rejects such uses with a clear error pointing at the missing import. -/
+
+@[expose] public section
+
+/--
+error: Cannot use attribute `[my_simp]`: module `UserAttr.BlaAttr` is loaded for IR only (reached as a private `meta` dependency). Add a non-private import of `UserAttr.BlaAttr`.
+-/
+#guard_msgs in
+@[my_simp]
+theorem midVal_eq : midVal = 17 := rfl
+
+end