diff --git a/program-runtime/src/loaded_programs.rs b/program-runtime/src/loaded_programs.rs
index ead152762da90f..4e5c1cdf50fd2f 100644
--- a/program-runtime/src/loaded_programs.rs
+++ b/program-runtime/src/loaded_programs.rs
@@ -483,6 +483,36 @@ impl LoadedPrograms {
         entry
     }
 
+    /// On the epoch boundary this removes all programs of the outdated feature set
+    pub fn prune_feature_set_transition(&mut self) {
+        for second_level in self.entries.values_mut() {
+            second_level.retain(|entry| {
+                let retain = match &entry.program {
+                    LoadedProgramType::Builtin(_) | LoadedProgramType::Closed => true,
+                    LoadedProgramType::LegacyV0(program) | LoadedProgramType::LegacyV1(program)
+                        if Arc::ptr_eq(
+                            program.get_loader(),
+                            &self.program_runtime_environment_v1,
+                        ) =>
+                    {
+                        true
+                    }
+                    LoadedProgramType::Unloaded(environment)
+                        if Arc::ptr_eq(environment, &self.program_runtime_environment_v1) =>
+                    {
+                        true
+                    }
+                    _ => false,
+                };
+                if !retain {
+                    self.stats.prunes.fetch_add(1, Ordering::Relaxed);
+                }
+                retain
+            });
+        }
+        self.remove_programs_with_no_entries();
+    }
+
     /// Before rerooting the blockstore this removes all programs of orphan forks
     pub fn prune<F: ForkGraph>(&mut self, fork_graph: &F, new_root: Slot) {
         let previous_root = self.latest_root;
diff --git a/programs/bpf_loader/src/syscalls/mod.rs b/programs/bpf_loader/src/syscalls/mod.rs
index 60db957d61877c..654d88114410b9 100644
--- a/programs/bpf_loader/src/syscalls/mod.rs
+++ b/programs/bpf_loader/src/syscalls/mod.rs
@@ -148,6 +148,8 @@ pub fn create_program_runtime_environment<'a>(
     debugging_features: bool,
 ) -> Result<BuiltinProgram<InvokeContext<'a>>, Error> {
     use rand::Rng;
+    // When adding new features for RBPF,
+    // also add them to `Bank::apply_builtin_program_feature_transitions()`.
     let config = Config {
         max_call_depth: compute_budget.max_call_depth,
         stack_frame_size: compute_budget.stack_frame_size,
diff --git a/runtime/src/bank.rs b/runtime/src/bank.rs
index df88a4255f9635..fb40449af36338 100644
--- a/runtime/src/bank.rs
+++ b/runtime/src/bank.rs
@@ -6286,17 +6286,6 @@ impl Bank {
         );
 
         if !debug_do_not_add_builtins {
-            let program_runtime_environment_v1 = create_program_runtime_environment(
-                &self.feature_set,
-                &self.runtime_config.compute_budget.unwrap_or_default(),
-                false, /* deployment */
-                false, /* debugging_features */
-            )
-            .unwrap();
-            self.loaded_programs_cache
-                .write()
-                .unwrap()
-                .program_runtime_environment_v1 = Arc::new(program_runtime_environment_v1);
             for builtin in BUILTINS
                 .iter()
                 .chain(additional_builtins.unwrap_or(&[]).iter())
@@ -7577,6 +7566,33 @@ impl Bank {
         only_apply_transitions_for_new_features: bool,
         new_feature_activations: &HashSet<Pubkey>,
     ) {
+        const FEATURES_AFFECTING_RBPF: &[Pubkey] = &[
+            feature_set::error_on_syscall_bpf_function_hash_collisions::id(),
+            feature_set::reject_callx_r10::id(),
+            feature_set::switch_to_new_elf_parser::id(),
+            feature_set::bpf_account_data_direct_mapping::id(),
+        ];
+        if !only_apply_transitions_for_new_features
+            || FEATURES_AFFECTING_RBPF
+                .iter()
+                .any(|key| new_feature_activations.contains(key))
+        {
+            let program_runtime_environment_v1 = create_program_runtime_environment(
+                &self.feature_set,
+                &self.runtime_config.compute_budget.unwrap_or_default(),
+                false, /* deployment */
+                false, /* debugging_features */
+            )
+            .unwrap();
+            let mut loaded_programs_cache = self.loaded_programs_cache.write().unwrap();
+            if *loaded_programs_cache.program_runtime_environment_v1
+                != program_runtime_environment_v1
+            {
+                loaded_programs_cache.program_runtime_environment_v1 =
+                    Arc::new(program_runtime_environment_v1);
+            }
+            loaded_programs_cache.prune_feature_set_transition();
+        }
         for builtin in BUILTINS.iter() {
             if let Some(feature_id) = builtin.feature_id {
                 let should_apply_action_for_feature_transition =
@@ -7598,7 +7614,6 @@ impl Bank {
                 }
             }
         }
-
         for precompile in get_precompiles() {
             #[allow(clippy::blocks_in_if_conditions)]
             if precompile.feature.map_or(false, |ref feature_id| {