diff --git a/crates/bashkit/src/interpreter/mod.rs b/crates/bashkit/src/interpreter/mod.rs
index c79612c9..4e6d333e 100644
--- a/crates/bashkit/src/interpreter/mod.rs
+++ b/crates/bashkit/src/interpreter/mod.rs
@@ -1002,6 +1002,21 @@ impl Interpreter {
         self.last_exit_code = state.last_exit_code;
         self.aliases = state.aliases.clone();
         self.traps = state.traps.clone();
+        // Recompute memory budget from restored state to prevent desync
+        let func_count = self.functions.len();
+        let func_bytes: usize = self
+            .functions
+            .values()
+            .map(|f| format!("{:?}", f.body).len())
+            .sum();
+        self.memory_budget = crate::limits::MemoryBudget::recompute_from_state(
+            &self.variables,
+            &self.arrays,
+            &self.assoc_arrays,
+            func_count,
+            func_bytes,
+            Self::is_internal_variable,
+        );
     }
 
     /// Get a reference to the current execution counters.
@@ -1377,6 +1392,7 @@ impl Interpreter {
                 let saved_exit = self.last_exit_code;
                 let saved_aliases = self.aliases.clone();
                 let saved_coproc = self.coproc_buffers.clone();
+                let saved_memory_budget = self.memory_budget.clone();
 
                 let mut result = self.execute_command_sequence(commands).await;
 
@@ -1420,6 +1436,7 @@ impl Interpreter {
                 self.last_exit_code = saved_exit;
                 self.aliases = saved_aliases;
                 self.coproc_buffers = saved_coproc;
+                self.memory_budget = saved_memory_budget;
 
                 // Consume Exit control flow at subshell boundary — exit only
                 // terminates the subshell, not the parent shell.
@@ -3982,6 +3999,7 @@ impl Interpreter {
         let saved_exit = self.last_exit_code;
         let saved_aliases = self.aliases.clone();
         let saved_coproc = self.coproc_buffers.clone();
+        let saved_memory_budget = self.memory_budget.clone();
 
         // Child only sees exported variables (env), not all shell variables.
         // Reset last_exit_code so $? starts at 0 (matches real bash subprocess).
@@ -4024,6 +4042,7 @@ impl Interpreter {
         self.last_exit_code = saved_exit;
         self.aliases = saved_aliases;
         self.coproc_buffers = saved_coproc;
+        self.memory_budget = saved_memory_budget;
         self.bash_source_stack = saved_source_stack;
         self.pipeline_stdin = prev_pipeline_stdin;
 
@@ -5968,6 +5987,7 @@ impl Interpreter {
                     let saved_assoc = self.assoc_arrays.clone();
                     let saved_aliases = self.aliases.clone();
                     let saved_cwd = self.cwd.clone();
+                    let saved_memory_budget = self.memory_budget.clone();
                     let mut stdout = String::new();
                     for cmd in commands {
                         let cmd_result = self.execute_command(cmd).await?;
@@ -5999,6 +6019,7 @@ impl Interpreter {
                     self.assoc_arrays = saved_assoc;
                     self.aliases = saved_aliases;
                     self.cwd = saved_cwd;
+                    self.memory_budget = saved_memory_budget;
                     self.counters.pop_function();
                     self.subst_generation += 1;
                     let trimmed = stdout.trim_end_matches('\n');
diff --git a/crates/bashkit/src/limits.rs b/crates/bashkit/src/limits.rs
index 251028c1..ff1a6a73 100644
--- a/crates/bashkit/src/limits.rs
+++ b/crates/bashkit/src/limits.rs
@@ -692,6 +692,40 @@ impl MemoryBudget {
         self.function_count = self.function_count.saturating_sub(1);
         self.function_body_bytes = self.function_body_bytes.saturating_sub(body_bytes);
     }
+
+    /// Recompute budget from actual variable/array state.
+    ///
+    /// Used after `restore_shell_state` where the budget was not serialized
+    /// alongside the snapshot. `is_internal` should return true for variable
+    /// names that are internal markers (not user-visible).
+    pub fn recompute_from_state<F>(
+        variables: &std::collections::HashMap<String, String>,
+        arrays: &std::collections::HashMap<String, std::collections::HashMap<usize, String>>,
+        assoc_arrays: &std::collections::HashMap<String, std::collections::HashMap<String, String>>,
+        function_count: usize,
+        function_body_bytes: usize,
+        is_internal: F,
+    ) -> Self
+    where
+        F: Fn(&str) -> bool,
+    {
+        let mut budget = Self::default();
+        for (k, v) in variables {
+            if !is_internal(k) {
+                budget.variable_count += 1;
+                budget.variable_bytes += k.len() + v.len();
+            }
+        }
+        for arr in arrays.values() {
+            budget.array_entries += arr.len();
+        }
+        for arr in assoc_arrays.values() {
+            budget.array_entries += arr.len();
+        }
+        budget.function_count = function_count;
+        budget.function_body_bytes = function_body_bytes;
+        budget
+    }
 }
 
 #[cfg(test)]
diff --git a/crates/bashkit/tests/spec_cases/bash/memory_budget_desync.test.sh b/crates/bashkit/tests/spec_cases/bash/memory_budget_desync.test.sh
new file mode 100644
index 00000000..2f948640
--- /dev/null
+++ b/crates/bashkit/tests/spec_cases/bash/memory_budget_desync.test.sh
@@ -0,0 +1,43 @@
+# Memory budget desync after subshell/command-substitution state restoration
+# Regression tests for issue #993
+
+### budget_accurate_after_command_substitutions
+# Memory budget should not inflate after many command substitutions.
+# After 100 command substitutions that create variables internally,
+# the parent shell should still be able to create variables.
+for i in $(seq 1 100); do
+  x=$(echo val)
+done
+# If budget were inflated, this would silently fail
+testvar="works"
+echo "$testvar"
+### expect
+works
+### end
+
+### budget_enforced_after_subshell
+# Memory budget should remain accurate after subshell execution.
+# Variables created in subshell should not affect parent budget.
+(
+  for i in $(seq 1 50); do
+    eval "sub_v$i=$i"
+  done
+)
+# Parent should still be able to create variables
+parentvar="ok"
+echo "$parentvar"
+### expect
+ok
+### end
+
+### subshell_vars_do_not_leak_budget
+# Creating and destroying variables in subshells should not
+# accumulate phantom budget entries.
+for i in $(seq 1 200); do
+  (eval "tmp_$i=value")
+done
+result="success"
+echo "$result"
+### expect
+success
+### end