diff --git a/components/esp_hw_support/port/esp32s31/esp_clk_tree.c b/components/esp_hw_support/port/esp32s31/esp_clk_tree.c
index 04c2c44c6d1..422a2c601a4 100644
--- a/components/esp_hw_support/port/esp32s31/esp_clk_tree.c
+++ b/components/esp_hw_support/port/esp32s31/esp_clk_tree.c
@@ -500,33 +500,31 @@ static const esp_clk_tree_gated_clk_t s_gated_ref_clks[] = {
 FORCE_INLINE_ATTR esp_err_t esp_clk_tree_enable_gated_clk(const esp_clk_tree_gated_clk_t *entry, bool enable)
 {
     int16_t prev_ref_cnt;
-    bool released_too_many = false;
 
+    /* Hold s_clk_tree_spinlock for refcnt only; parent/gate (may take PERIPH_RCC)
+     * run outside to avoid clk_tree <-> PERIPH_RCC deadlock. */
     esp_os_enter_critical(&s_clk_tree_spinlock);
     if (enable) {
         prev_ref_cnt = s_mod_clk_gate_ref_cnt[entry->clk_id]++;
-        if (prev_ref_cnt == 0) {
-            if (entry->parent_power != NULL) {
-                entry->parent_power(true);
-            }
-            ENABLE_CLK_GATE(entry->set_gate, true);
-        }
     } else {
         prev_ref_cnt = s_mod_clk_gate_ref_cnt[entry->clk_id]--;
         if (prev_ref_cnt <= 0) {
             s_mod_clk_gate_ref_cnt[entry->clk_id] = 0;
-            released_too_many = true;
-        } else if (prev_ref_cnt == 1) {
-            ENABLE_CLK_GATE(entry->set_gate, false);
-            if (entry->parent_power != NULL) {
-                entry->parent_power(false);
-            }
+            esp_os_exit_critical(&s_clk_tree_spinlock);
+            ESP_LOGW(TAG, "soc_module_clk_t %d disabled multiple times!!", entry->clk_id);
+            return ESP_OK;
         }
     }
     esp_os_exit_critical(&s_clk_tree_spinlock);
 
-    if (released_too_many) {
-        ESP_LOGW(TAG, "soc_module_clk_t %d disabled multiple times!!", entry->clk_id);
+    if ((enable && prev_ref_cnt == 0) || (!enable && prev_ref_cnt == 1)) {
+        if (enable && entry->parent_power != NULL) {
+            entry->parent_power(true);
+        }
+        ENABLE_CLK_GATE(entry->set_gate, enable);
+        if (!enable && entry->parent_power != NULL) {
+            entry->parent_power(false);
+        }
     }
     return ESP_OK;
 }
diff --git a/components/esp_security/src/esp_crypto_periph_clk.c b/components/esp_security/src/esp_crypto_periph_clk.c
index cdd65057c12..bc5ec97c666 100644
--- a/components/esp_security/src/esp_crypto_periph_clk.c
+++ b/components/esp_security/src/esp_crypto_periph_clk.c
@@ -48,8 +48,10 @@ int __DECLARE_RCC_ATOMIC_ENV __attribute__((unused));
 #if SOC_AES_SUPPORTED
 void esp_crypto_aes_enable_periph_clk(bool enable)
 {
+    if (enable) {
+        esp_crypto_common_clk_enable(true);
+    }
     AES_RCC_ATOMIC() {
-        esp_crypto_common_clk_enable(enable);
         aes_ll_enable_bus_clock(enable);
         if (enable) {
             aes_ll_reset_register();
@@ -61,14 +63,19 @@ void esp_crypto_aes_enable_periph_clk(bool enable)
         }
 #endif
     }
+    if (!enable) {
+        esp_crypto_common_clk_enable(false);
+    }
 }
 #endif
 
 #if SOC_SHA_SUPPORTED
 void esp_crypto_sha_enable_periph_clk(bool enable)
 {
+    if (enable) {
+        esp_crypto_common_clk_enable(true);
+    }
     SHA_RCC_ATOMIC() {
-        esp_crypto_common_clk_enable(enable);
         sha_ll_enable_bus_clock(enable);
         if (enable) {
             sha_ll_reset_register();
@@ -80,14 +87,19 @@ void esp_crypto_sha_enable_periph_clk(bool enable)
         }
 #endif
     }
+    if (!enable) {
+        esp_crypto_common_clk_enable(false);
+    }
 }
 #endif
 
 #if SOC_MPI_SUPPORTED
 void esp_crypto_mpi_enable_periph_clk(bool enable)
 {
+    if (enable) {
+        esp_crypto_common_clk_enable(true);
+    }
     MPI_RCC_ATOMIC() {
-        esp_crypto_common_clk_enable(enable);
         mpi_ll_enable_bus_clock(enable);
         if (enable) {
             mpi_ll_power_up();
@@ -96,14 +108,19 @@ void esp_crypto_mpi_enable_periph_clk(bool enable)
             mpi_ll_power_down();
         }
     }
+    if (!enable) {
+        esp_crypto_common_clk_enable(false);
+    }
 }
 #endif
 
 #if SOC_ECC_SUPPORTED
 void esp_crypto_ecc_enable_periph_clk(bool enable)
 {
+    if (enable) {
+        esp_crypto_common_clk_enable(true);
+    }
     ECC_RCC_ATOMIC() {
-        esp_crypto_common_clk_enable(enable);
         ecc_ll_enable_bus_clock(enable);
         if (enable) {
             ecc_ll_power_up();
@@ -112,53 +129,73 @@ void esp_crypto_ecc_enable_periph_clk(bool enable)
             ecc_ll_power_down();
         }
     }
+    if (!enable) {
+        esp_crypto_common_clk_enable(false);
+    }
 }
 #endif
 
 #if SOC_HMAC_SUPPORTED && !CONFIG_IDF_TARGET_ESP32S2
 void esp_crypto_hmac_enable_periph_clk(bool enable)
 {
+    if (enable) {
+        esp_crypto_common_clk_enable(true);
+    }
     HMAC_RCC_ATOMIC() {
-        esp_crypto_common_clk_enable(enable);
         hmac_ll_enable_bus_clock(enable);
         if (enable) {
             hmac_ll_reset_register();
         }
     }
+    if (!enable) {
+        esp_crypto_common_clk_enable(false);
+    }
 }
 #endif
 
 #if SOC_DIG_SIGN_SUPPORTED && !CONFIG_IDF_TARGET_ESP32S2
 void esp_crypto_ds_enable_periph_clk(bool enable)
 {
+    if (enable) {
+        esp_crypto_common_clk_enable(true);
+    }
     DS_RCC_ATOMIC() {
-        esp_crypto_common_clk_enable(enable);
         ds_ll_enable_bus_clock(enable);
         if (enable) {
             ds_ll_reset_register();
         }
     }
+    if (!enable) {
+        esp_crypto_common_clk_enable(false);
+    }
 }
 #endif
 
 #if SOC_ECDSA_SUPPORTED
 void esp_crypto_ecdsa_enable_periph_clk(bool enable)
 {
+    if (enable) {
+        esp_crypto_common_clk_enable(true);
+    }
     ECDSA_RCC_ATOMIC() {
-        esp_crypto_common_clk_enable(enable);
         ecdsa_ll_enable_bus_clock(enable);
         if (enable) {
             ecdsa_ll_reset_register();
         }
     }
+    if (!enable) {
+        esp_crypto_common_clk_enable(false);
+    }
 }
 #endif
 
 #if SOC_KEY_MANAGER_SUPPORT_KEY_DEPLOYMENT
 void esp_crypto_key_mgr_enable_periph_clk(bool enable)
 {
+    if (enable) {
+        esp_crypto_common_clk_enable(true);
+    }
     KEY_MANAGER_RCC_ATOMIC() {
-        esp_crypto_common_clk_enable(enable);
         key_mgr_ll_power_up();
         key_mgr_ll_enable_bus_clock(enable);
         key_mgr_ll_enable_peripheral_clock(enable);
@@ -166,5 +203,8 @@ void esp_crypto_key_mgr_enable_periph_clk(bool enable)
             key_mgr_ll_reset_register();
         }
     }
+    if (!enable) {
+        esp_crypto_common_clk_enable(false);
+    }
 }
 #endif