diff --git a/resources/report/js/filters.js b/resources/report/js/filters.js
index 5eba1307..d725a306 100644
--- a/resources/report/js/filters.js
+++ b/resources/report/js/filters.js
@@ -2,6 +2,9 @@ var filters = {
     /* Filter functions return true if the given plugin passes the filter and
        should be displayed, otherwise false. */
 
+    hiddenPluginNo: 0,
+    hiddenMessageNo: 0,
+
     searchFilter: function(plugin, needle) {
         if (needle.length == 0) {
             return true;
@@ -29,23 +32,31 @@ var filters = {
     },
 
     messagelessFilter: function(plugin) {
-        if (document.getElementById('hideMessagelessPlugins').checked) {
-            /* If any messages exist, check if they are hidden or not. Note
-               that the messages may not be present as elements, so the check
-               is actually if they would be hidden according to the message
-               filters. */
+        /* This function could be further optimised to perform fewer checks,
+           but it's also responsible for setting the hidden message count, so
+           has to go through everything. */
 
-            if (this.allMessageFilter()) {
-                for (var i = 0; i < plugin.messages.length; ++i) {
-                    if (this.noteFilter(plugin.messages[i])
-                        && this.doNotCleanFilter(plugin.messages[i])) {
+        var hasMessages = false;
+        /* If any messages exist, check if they are hidden or not. Note
+           that the messages may not be present as elements, so the check
+           is actually if they would be hidden according to the message
+           filters. */
+        if (this.allMessageFilter()) {
+            plugin.messages.forEach(function(message){
+                if (this.noteFilter(message)
+                    && this.doNotCleanFilter(message)) {
 
-                        return true;
-                    }
+                    hasMessages = true;
+                    return;
                 }
-            }
+                ++hiddenMessageNo;
+            }, this);
+        } else {
+            hiddenMessageNo += plugin.messages.length;
+        }
 
-            return false;
+        if (document.getElementById('hideMessagelessPlugins').checked) {
+            return hasMessages;
         } else {
             return true;
         }
@@ -53,10 +64,12 @@ var filters = {
 
     applyPluginFilters: function(plugins) {
         var search = document.getElementById('searchBox').value.toLowerCase();
-        var hiddenPluginNo = 0;
+        hiddenPluginNo = 0;
+        hiddenMessageNo = 0;
         var filteredPlugins = [];
 
         plugins.forEach(function(plugin){
+            /* Messageless filter needs to run first. */
             if (this.messagelessFilter(plugin)
                 && this.searchFilter(plugin, search)) {
 
@@ -67,6 +80,7 @@ var filters = {
         }, this);
 
         document.getElementById('hiddenPluginNo').textContent = hiddenPluginNo;
+        document.getElementById('hiddenMessageNo').textContent = hiddenMessageNo;
 
         return filteredPlugins;
     },
@@ -96,7 +110,6 @@ var filters = {
     },
 
     applyMessageFilters: function(messages) {
-        var hiddenMessageNo = 0;
         var filteredMessages = [];
 
         if (this.allMessageFilter()) {
@@ -107,12 +120,9 @@ var filters = {
                     filteredMessages.push(message);
                     return;
                 }
-                ++hiddenMessageNo;
             }, this);
         }
 
-        document.getElementById('hiddenMessageNo').textContent = hiddenMessageNo;
-
         return filteredMessages;
     },
 };
@@ -121,4 +131,10 @@ function setFilteredUIData(evt) {
     var filtered = filters.applyPluginFilters(loot.game.plugins);
     document.getElementById('cardsNav').lastElementChild.data = filtered;
     document.getElementById('main').lastElementChild.data = filtered;
+
+    /* Also run message filters on the current card elements. */
+    var cards = document.getElementById('main').getElementsByTagName('loot-plugin-card');
+    for (var i = 0; i < cards.length; ++i) {
+        cards[i].onMessagesChange();  // Calls Plugin.getUIMessages(), which calls filters.applyMessageFilters().
+    }
 }
\ No newline at end of file
diff --git a/resources/report/js/plugin.js b/resources/report/js/plugin.js
index 7c295f43..609affc6 100644
--- a/resources/report/js/plugin.js
+++ b/resources/report/js/plugin.js
@@ -116,7 +116,8 @@ function Plugin(obj) {
         var uiMessages = [];
         /* Now add the new messages. */
         if (this.messages && this.messages.length != 0) {
-            this.messages.forEach(function(message) {
+            var messages = filters.applyMessageFilters(this.messages);
+            messages.forEach(function(message) {
                 var messageLi = document.createElement('li');
                 messageLi.className = message.type;
                 // Use the Marked library for Markdown formatting support.
diff --git a/resources/report/js/script.js b/resources/report/js/script.js
index e82d79d2..0d7d991e 100644
--- a/resources/report/js/script.js
+++ b/resources/report/js/script.js
@@ -1105,10 +1105,10 @@ function setupEventHandlers() {
     document.getElementById('hideVersionNumbers').addEventListener('change', toggleDisplayCSS, false);
     document.getElementById('hideCRCs').addEventListener('change', toggleDisplayCSS, false);
     document.getElementById('hideBashTags').addEventListener('change', toggleDisplayCSS, false);
-    document.getElementById('hideNotes').addEventListener('change', applyFilters, false);
-    document.getElementById('hideDoNotCleanMessages').addEventListener('change', applyFilters, false);
+    document.getElementById('hideNotes').addEventListener('change', setFilteredUIData, false);
+    document.getElementById('hideDoNotCleanMessages').addEventListener('change', setFilteredUIData, false);
     document.getElementById('hideInactivePluginMessages').addEventListener('change', applyFilters, false);
-    document.getElementById('hideAllPluginMessages').addEventListener('change', applyFilters, false);
+    document.getElementById('hideAllPluginMessages').addEventListener('change', setFilteredUIData, false);
     document.getElementById('hideMessagelessPlugins').addEventListener('change', setFilteredUIData, false);
     document.body.addEventListener('loot-filter-conflicts', handleConflictsFilter, false);