diff --git a/public/script.js b/public/script.js
index 48bf112a6..b5fadcdc1 100644
--- a/public/script.js
+++ b/public/script.js
@@ -1993,9 +1993,10 @@ export async function sendTextareaMessage() {
  * @param {boolean} isUser If the message was sent by the user
  * @param {number} messageId Message index in chat array
  * @param {object} [sanitizerOverrides] DOMPurify sanitizer option overrides
+ * @param {boolean} [isReasoning] If the message is reasoning output
  * @returns {string} HTML string
  */
-export function messageFormatting(mes, ch_name, isSystem, isUser, messageId, sanitizerOverrides = {}) {
+export function messageFormatting(mes, ch_name, isSystem, isUser, messageId, sanitizerOverrides = {}, isReasoning = false) {
     if (!mes) {
         return '';
     }
@@ -2029,6 +2030,9 @@ export function messageFormatting(mes, ch_name, isSystem, isUser, messageId, san
     if (!isSystem) {
         function getRegexPlacement() {
             try {
+                if (isReasoning) {
+                    return regex_placement.REASONING;
+                }
                 if (isUser) {
                     return regex_placement.USER_INPUT;
                 } else if (chat[messageId]?.extra?.type === 'narrator') {
@@ -2250,8 +2254,8 @@ function getMessageFromTemplate({
 export function updateMessageBlock(messageId, message) {
     const messageElement = $(`#chat [mesid="${messageId}"]`);
     const text = message?.extra?.display_text ?? message.mes;
-    messageElement.find('.mes_text').html(messageFormatting(text, message.name, message.is_system, message.is_user, messageId));
-    messageElement.find('.mes_reasoning').html(messageFormatting(message.extra?.reasoning ?? '', '', false, false, -1));
+    messageElement.find('.mes_text').html(messageFormatting(text, message.name, message.is_system, message.is_user, messageId, {}, false));
+    messageElement.find('.mes_reasoning').html(messageFormatting(message.extra?.reasoning ?? '', '', false, false, messageId, {}, true));
     addCopyToCodeBlocks(messageElement);
     appendMediaToMessage(message, messageElement);
 }
@@ -2408,9 +2412,10 @@ export function addOneMessage(mes, { type = 'normal', insertAfter = null, scroll
         mes.is_user,
         chat.indexOf(mes),
         sanitizerOverrides,
+        false,
     );
-    const bias = messageFormatting(mes.extra?.bias ?? '', '', false, false, -1);
-    const reasoning = messageFormatting(mes.extra?.reasoning ?? '', '', false, false, -1);
+    const bias = messageFormatting(mes.extra?.bias ?? '', '', false, false, -1, {}, false);
+    const reasoning = messageFormatting(mes.extra?.reasoning ?? '', '', false, false, chat.indexOf(mes), {}, true);
     let bookmarkLink = mes?.extra?.bookmark_link ?? '';
 
     let params = {
@@ -3205,7 +3210,7 @@ class StreamingProcessor {
             if (this.reasoning) {
                 chat[messageId]['extra']['reasoning'] = this.reasoning;
                 if (this.messageReasoningDom instanceof HTMLElement) {
-                    const formattedReasoning = messageFormatting(this.reasoning, '', false, false, -1);
+                    const formattedReasoning = messageFormatting(this.reasoning, '', false, false, messageId, {}, true);
                     this.messageReasoningDom.innerHTML = formattedReasoning;
                 }
             }
@@ -3232,6 +3237,8 @@ class StreamingProcessor {
                 chat[messageId].is_system,
                 chat[messageId].is_user,
                 messageId,
+                {},
+                false,
             );
             if (this.messageTextDom instanceof HTMLElement) {
                 this.messageTextDom.innerHTML = formattedText;
@@ -3383,7 +3390,7 @@ class StreamingProcessor {
                 if (logprobs) {
                     this.messageLogprobs.push(...(Array.isArray(logprobs) ? logprobs : [logprobs]));
                 }
-                this.reasoning = state?.reasoning ?? '';
+                this.reasoning = getRegexedString(state?.reasoning ?? '', regex_placement.REASONING);
                 await eventSource.emit(event_types.STREAM_TOKEN_RECEIVED, text);
                 await sw.tick(() => this.onProgressStreaming(this.messageId, this.continueMessage + text));
             }
@@ -3850,14 +3857,6 @@ export async function Generate(type, { automatic_trigger, force_name2, quiet_pro
         coreChat.pop();
     }
 
-    const reasoning = new PromptReasoning();
-    for (let i = coreChat.length - 1; i >= 0; i--) {
-        if (reasoning.isLimitReached()) {
-            break;
-        }
-        coreChat[i] = { ...coreChat[i], mes: reasoning.addToMessage(coreChat[i].mes, coreChat[i].extra?.reasoning) };
-    }
-
     coreChat = await Promise.all(coreChat.map(async (chatItem, index) => {
         let message = chatItem.mes;
         let regexType = chatItem.is_user ? regex_placement.USER_INPUT : regex_placement.AI_OUTPUT;
@@ -3877,6 +3876,25 @@ export async function Generate(type, { automatic_trigger, force_name2, quiet_pro
         };
     }));
 
+    const reasoning = new PromptReasoning();
+    for (let i = coreChat.length - 1; i >= 0; i--) {
+        if (reasoning.isLimitReached()) {
+            break;
+        }
+        const depth = coreChat.length - i - 1;
+        coreChat[i] = {
+            ...coreChat[i],
+            mes: reasoning.addToMessage(
+                coreChat[i].mes,
+                getRegexedString(
+                    String(coreChat[i].extra?.reasoning ?? ''),
+                    regex_placement.REASONING,
+                    { isPrompt: true, depth: depth },
+                ),
+            ),
+        };
+    }
+
     // Determine token limit
     let this_max_context = getMaxContextSize();
 
@@ -4785,6 +4803,7 @@ export async function Generate(type, { automatic_trigger, force_name2, quiet_pro
         const swipes = extractMultiSwipes(data, type);
 
         messageChunk = cleanUpMessage(getMessage, isImpersonate, isContinue, false);
+        reasoning = getRegexedString(reasoning, regex_placement.REASONING);
 
         if (isContinue) {
             getMessage = continue_mag + getMessage;
@@ -7190,9 +7209,11 @@ function messageEditAuto(div) {
         mes.is_system,
         mes.is_user,
         this_edit_mes_id,
+        {},
+        false,
     ));
     mesBlock.find('.mes_bias').empty();
-    mesBlock.find('.mes_bias').append(messageFormatting(bias, '', false, false, -1));
+    mesBlock.find('.mes_bias').append(messageFormatting(bias, '', false, false, -1, {}, false));
     saveChatDebounced();
 }
 
@@ -7214,10 +7235,12 @@ async function messageEditDone(div) {
             mes.is_system,
             mes.is_user,
             this_edit_mes_id,
+            {},
+            false,
         ),
     );
     mesBlock.find('.mes_bias').empty();
-    mesBlock.find('.mes_bias').append(messageFormatting(bias, '', false, false, -1));
+    mesBlock.find('.mes_bias').append(messageFormatting(bias, '', false, false, -1, {}, false));
     appendMediaToMessage(mes, div.closest('.mes'));
     addCopyToCodeBlocks(div.closest('.mes'));
 
@@ -10860,6 +10883,8 @@ jQuery(async function () {
                 chat[this_edit_mes_id].is_system,
                 chat[this_edit_mes_id].is_user,
                 this_edit_mes_id,
+                {},
+                false,
             ));
         appendMediaToMessage(chat[this_edit_mes_id], $(this).closest('.mes'));
         addCopyToCodeBlocks($(this).closest('.mes'));
diff --git a/public/scripts/extensions/regex/editor.html b/public/scripts/extensions/regex/editor.html
index 9e699a622..8cfe9e008 100644
--- a/public/scripts/extensions/regex/editor.html
+++ b/public/scripts/extensions/regex/editor.html
@@ -94,6 +94,12 @@
                         <span data-i18n="World Info">World Info</span>
                     </label>
                 </div>
+                <div data-i18n="[title]ext_regex_reasoning_desc" title="Reasoning block contents. When 'Only Format Prompt' is checked, it will also affect the reasoning contents added to the prompt.">
+                    <label class="checkbox flex-container">
+                        <input type="checkbox" name="replace_position" value="6">
+                        <span data-i18n="Reasoning">Reasoning</span>
+                    </label>
+                </div>
                 <div class="flex-container wide100p marginTop5">
                     <div class="flex1 flex-container flexNoGap">
                         <small data-i18n="[title]ext_regex_min_depth_desc" title="When applied to prompts or display, only affect messages that are at least N levels deep. 0 = last message, 1 = penultimate message, etc. Only counts WI entries @Depth and usable messages, i.e. not hidden or system.">
diff --git a/public/scripts/extensions/regex/engine.js b/public/scripts/extensions/regex/engine.js
index 8c28d01f3..f6e22d249 100644
--- a/public/scripts/extensions/regex/engine.js
+++ b/public/scripts/extensions/regex/engine.js
@@ -20,6 +20,7 @@ const regex_placement = {
     SLASH_COMMAND: 3,
     // 4 - sendAs (legacy)
     WORLD_INFO: 5,
+    REASONING: 6,
 };
 
 export const substitute_find_regex = {
@@ -94,7 +95,7 @@ function getRegexedString(rawString, placement, { characterOverride, isMarkdown,
             // Script applies to Generate and input is Generate
             (script.promptOnly && isPrompt) ||
             // Script applies to all cases when neither "only"s are true, but there's no need to do it when `isMarkdown`, the as source (chat history) should already be changed beforehand
-            (!script.markdownOnly && !script.promptOnly && !isMarkdown)
+            (!script.markdownOnly && !script.promptOnly && !isMarkdown && !isPrompt)
         ) {
             if (isEdit && !script.runOnEdit) {
                 console.debug(`getRegexedString: Skipping script ${script.scriptName} because it does not run on edit`);
diff --git a/public/scripts/extensions/regex/index.js b/public/scripts/extensions/regex/index.js
index 73538e4ed..8ac6ae6d6 100644
--- a/public/scripts/extensions/regex/index.js
+++ b/public/scripts/extensions/regex/index.js
@@ -18,7 +18,7 @@ import { t } from '../../i18n.js';
  * @property {string} replaceString - The replace string
  * @property {string[]} trimStrings - The trim strings
  * @property {string?} findRegex - The find regex
- * @property {string?} substituteRegex - The substitute regex
+ * @property {number?} substituteRegex - The substitute regex
  */
 
 /**
diff --git a/public/scripts/reasoning.js b/public/scripts/reasoning.js
index 19dc024a6..888276f8e 100644
--- a/public/scripts/reasoning.js
+++ b/public/scripts/reasoning.js
@@ -1,4 +1,5 @@
 import { chat, closeMessageEditor, saveChatConditional, saveSettingsDebounced, substituteParams, updateMessageBlock } from '../script.js';
+import { getRegexedString, regex_placement } from './extensions/regex/engine.js';
 import { t } from './i18n.js';
 import { MacrosParser } from './macros.js';
 import { Popup } from './popup.js';
@@ -224,7 +225,7 @@ function setReasoningEventHandlers(){
         }
 
         const textarea = messageBlock.find('.reasoning_edit_textarea');
-        const reasoning = String(textarea.val());
+        const reasoning = getRegexedString(String(textarea.val()), regex_placement.REASONING, { isEdit: true });
         message.extra.reasoning = reasoning;
         await saveChatConditional();
         updateMessageBlock(messageId, message);