diff --git a/src/megatron/bridge/recipes/deepseek/deepseek_v3.py b/src/megatron/bridge/recipes/deepseek/deepseek_v3.py
index c31ecbc0bc..10f804432d 100644
--- a/src/megatron/bridge/recipes/deepseek/deepseek_v3.py
+++ b/src/megatron/bridge/recipes/deepseek/deepseek_v3.py
@@ -101,9 +101,9 @@ def deepseek_v3_pretrain_config() -> ConfigContainer:
     set_deepseek_v3_pipeline_model_parallel_layout(cfg.model)
 
     # MoE Token Dispatcher settings
-    cfg.model.moe_token_dispatcher_type = "alltoall"  # Default from DeepSeekModelProvider
-    apply_flex_dispatcher_backend(cfg.model, None)
-    cfg.model.moe_flex_dispatcher_backend = "deepep"  # Options: None, deepep, hybridep
+    # Note: moe_token_dispatcher_type may be overridden by apply_flex_dispatcher_backend at the end
+    cfg.model.moe_token_dispatcher_type = "alltoall"
+    cfg.model.moe_flex_dispatcher_backend = "hybridep"  # Options: None, deepep, hybridep
     cfg.model.moe_hybridep_num_sms = 16  # Number of SMs for hybridep backend
 
     # Training config (DIFFERENT from _pretrain_common)
@@ -168,6 +168,7 @@ def deepseek_v3_pretrain_config() -> ConfigContainer:
     cfg.comm_overlap = CommOverlapConfig(tp_comm_overlap=False)
     cfg.comm_overlap.delay_wgrad_compute = False
     cfg.comm_overlap.overlap_moe_expert_parallel_comm = False
+    # Note: moe_shared_expert_overlap may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_shared_expert_overlap = True  # Default from DeepSeekModelProvider
 
     # Checkpoint config (DIFFERENT from _pretrain_common: save_interval=2000 vs 500)
@@ -192,6 +193,8 @@ def deepseek_v3_pretrain_config() -> ConfigContainer:
     if cfg.model.apply_rope_fusion:
         cfg.dist.enable_megatron_core_experimental = True  # mla rope fusion is experimental
 
+    apply_flex_dispatcher_backend(cfg.model, cfg.model.moe_flex_dispatcher_backend)
+
     return cfg
 
 
@@ -248,9 +251,9 @@ def deepseek_v3_pretrain_config_32nodes() -> ConfigContainer:
     set_deepseek_v3_pipeline_model_parallel_layout(cfg.model)
 
     # MoE Token Dispatcher settings
+    # Note: moe_token_dispatcher_type may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_token_dispatcher_type = "alltoall"
-    apply_flex_dispatcher_backend(cfg.model, None)
-    cfg.model.moe_flex_dispatcher_backend = "deepep"
+    cfg.model.moe_flex_dispatcher_backend = "hybridep"  # Options: None, deepep, hybridep
     cfg.model.moe_hybridep_num_sms = 16
 
     # Training config
@@ -310,6 +313,7 @@ def deepseek_v3_pretrain_config_32nodes() -> ConfigContainer:
     cfg.comm_overlap = CommOverlapConfig(tp_comm_overlap=False)
     cfg.comm_overlap.delay_wgrad_compute = False
     cfg.comm_overlap.overlap_moe_expert_parallel_comm = False
+    # Note: moe_shared_expert_overlap may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_shared_expert_overlap = True
 
     # Checkpoint config
@@ -331,4 +335,6 @@ def deepseek_v3_pretrain_config_32nodes() -> ConfigContainer:
     if cfg.model.apply_rope_fusion:
         cfg.dist.enable_megatron_core_experimental = True  # mla rope fusion is experimental
 
+    apply_flex_dispatcher_backend(cfg.model, cfg.model.moe_flex_dispatcher_backend)
+
     return cfg
diff --git a/src/megatron/bridge/recipes/qwen/qwen3_moe.py b/src/megatron/bridge/recipes/qwen/qwen3_moe.py
index 3c8af8802d..10d6069b33 100644
--- a/src/megatron/bridge/recipes/qwen/qwen3_moe.py
+++ b/src/megatron/bridge/recipes/qwen/qwen3_moe.py
@@ -153,8 +153,9 @@ def qwen3_30b_a3b_pretrain_config() -> ConfigContainer:
     cfg.model.init_method_std = 0.02
 
     # MoE Token Dispatcher settings
+    # Note: moe_token_dispatcher_type may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_token_dispatcher_type = "alltoall"
-    cfg.model.moe_flex_dispatcher_backend = "deepep"
+    cfg.model.moe_flex_dispatcher_backend = "deepep"  # Options: None, deepep, hybridep
     cfg.model.moe_hybridep_num_sms = 16
 
     # Training config
@@ -205,6 +206,7 @@ def qwen3_30b_a3b_pretrain_config() -> ConfigContainer:
     # cfg.comm_overlap = CommOverlapConfig(tp_comm_overlap=False)  # Uncomment to enable
     # cfg.comm_overlap.delay_wgrad_compute = False  # Delay wgrad compute for overlap
     # cfg.comm_overlap.overlap_moe_expert_parallel_comm = False  # MoE-specific: Overlap EP communication
+    # Note: moe_shared_expert_overlap may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_shared_expert_overlap = False  # Overlap shared expert computation
 
     # Checkpoint config (paths set in _pretrain_common)
@@ -222,6 +224,8 @@ def qwen3_30b_a3b_pretrain_config() -> ConfigContainer:
     # MoE Force Load Balancing
     cfg.model.moe_router_force_load_balancing = False
 
+    apply_flex_dispatcher_backend(cfg.model, cfg.model.moe_flex_dispatcher_backend)
+
     return cfg
 
 
@@ -262,6 +266,7 @@ def qwen3_235b_a22b_pretrain_config() -> ConfigContainer:
     cfg.model.account_for_loss_in_pipeline_split = True
 
     # MoE Token Dispatcher settings
+    # Note: moe_token_dispatcher_type may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_token_dispatcher_type = "alltoall"
     cfg.model.moe_flex_dispatcher_backend = "deepep"
     cfg.model.moe_hybridep_num_sms = 16
@@ -314,6 +319,7 @@ def qwen3_235b_a22b_pretrain_config() -> ConfigContainer:
     # cfg.comm_overlap = CommOverlapConfig(tp_comm_overlap=False)  # Uncomment to enable
     # cfg.comm_overlap.delay_wgrad_compute = False
     # cfg.comm_overlap.overlap_moe_expert_parallel_comm = False
+    # Note: moe_shared_expert_overlap may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_shared_expert_overlap = False  # Overlap shared expert computation
 
     # Checkpoint config
@@ -331,6 +337,8 @@ def qwen3_235b_a22b_pretrain_config() -> ConfigContainer:
     # MoE Force Load Balancing
     cfg.model.moe_router_force_load_balancing = False
 
+    apply_flex_dispatcher_backend(cfg.model, cfg.model.moe_flex_dispatcher_backend)
+
     return cfg
 
 
diff --git a/src/megatron/bridge/recipes/qwen/qwen3_next.py b/src/megatron/bridge/recipes/qwen/qwen3_next.py
index f21f2f5bcc..ef2f527694 100644
--- a/src/megatron/bridge/recipes/qwen/qwen3_next.py
+++ b/src/megatron/bridge/recipes/qwen/qwen3_next.py
@@ -148,11 +148,10 @@ def qwen3_next_80b_a3b_pretrain_config() -> ConfigContainer:
     cfg.model.mtp_loss_scaling_factor = 0.1  # Loss scaling factor for MTP
 
     # MoE Token Dispatcher settings
+    # Note: moe_token_dispatcher_type may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_token_dispatcher_type = "alltoall"  # Options: alltoall, allgather, flex
-    cfg.model.moe_flex_dispatcher_backend = (
-        "deepep"  # Options: None, deepep, hybridep (default from TransformerConfig)
-    )
-    cfg.model.moe_hybridep_num_sms = 16  # Number of SMs for hybridep backend (default from TransformerConfig)
+    cfg.model.moe_flex_dispatcher_backend = "deepep"  # Options: None, deepep, hybridep
+    cfg.model.moe_hybridep_num_sms = 16  # Number of SMs for hybridep backend
 
     # Training config
     cfg.train.manual_gc = True
@@ -205,6 +204,7 @@ def qwen3_next_80b_a3b_pretrain_config() -> ConfigContainer:
     # cfg.comm_overlap = CommOverlapConfig(tp_comm_overlap=False)  # Uncomment to enable
     # cfg.comm_overlap.delay_wgrad_compute = False  # Delay wgrad compute for overlap
     # cfg.comm_overlap.overlap_moe_expert_parallel_comm = False  # MoE-specific: Overlap EP communication
+    # Note: moe_shared_expert_overlap may be overridden by apply_flex_dispatcher_backend at the end
     cfg.model.moe_shared_expert_overlap = False  # Overlap shared expert computation
 
     # Checkpoint config
@@ -222,6 +222,8 @@ def qwen3_next_80b_a3b_pretrain_config() -> ConfigContainer:
     # MoE Force Load Balancing
     cfg.model.moe_router_force_load_balancing = False
 
+    apply_flex_dispatcher_backend(cfg.model, cfg.model.moe_flex_dispatcher_backend)
+
     return cfg