diff --git a/src/atcore.cpp b/src/atcore.cpp
--- a/src/atcore.cpp
+++ b/src/atcore.cpp
@@ -473,13 +473,13 @@
 void AtCore::pause(const QString &pauseActions)
 {
     pushCommand(GCode::toCommand(GCode::M114));
-    setState(AtCore::PAUSE);
     if (!pauseActions.isEmpty()) {
         QStringList temp = pauseActions.split(QChar::fromLatin1(','));
-        for (int i = 0; i < temp.length(); i++) {
+        for (int i = 0; i < temp.count(); i++) {
             pushCommand(temp.at(i));
         }
     }
+    setState(AtCore::PAUSE);
 }
 
 void AtCore::resume()
@@ -520,7 +520,6 @@
     } else {
         pushCommand(GCode::toCommand(GCode::M104, QString::number(extruder), QString::number(temp)));
     }
-    temperature().setExtruderTargetTemperature(temp);
 }
 
 void AtCore::setBedTemp(uint temp, bool andWait)
@@ -530,7 +529,6 @@
     } else {
         pushCommand(GCode::toCommand(GCode::M140, QString::number(temp)));
     }
-    temperature().setBedTargetTemperature(temp);
 }
 
 void AtCore::setFanSpeed(uint speed, uint fanNumber)
diff --git a/src/printthread.h b/src/printthread.h
--- a/src/printthread.h
+++ b/src/printthread.h
@@ -101,5 +101,27 @@
      * @brief end the print
      */
     void endPrint();
+
+    /**
+     * @brief injectCommand Attempt to inject Command into the job from the currently printing file.
+     *
+     *
+     * Inject one of the following: line must start with ';#'
+     * example line ;# showMessage: Hello
+     * - pause:Comma seperated post pause commands - Pause the print job send comma seperated commands.
+     * - setExtTemp:Temp,extruder number,wait - set extruder Temperature. Use true or false for wait
+     * - setBedTemp:Temp,wait - Set the bed Temperature. Use true or false for wait
+     * - setFanSpeed:speed, Fan# - set fan#'s speed range: 0-255.
+     * - setPrintSpeed:speed - set print speed range: 0-100.
+     * - setFlowRate:rate - set FlowRate range: 0-100.
+     * - showMessage:message - Show message on printer's LCD
+     * - Command:command - inject your own command. Command is sent as is to be sure you line is correct.
+     * @param command a valid command Begins with ;#
+     */
+    void injectCommand(QString command);
+
+    /**
+     * @brief d: Private storage for the thread
+     */
     PrintThreadPrivate *d;
 };
diff --git a/src/printthread.cpp b/src/printthread.cpp
--- a/src/printthread.cpp
+++ b/src/printthread.cpp
@@ -80,7 +80,7 @@
         while (d->cline.isEmpty() && !d->gcodestream->atEnd()) {
             nextLine();
         }
-        if (!d->cline.isEmpty()) {
+        if (!d->cline.isEmpty() && d->core->state() != AtCore::PAUSE) {
             qCDebug(PRINT_THREAD) << "cline:" << d->cline;
             emit nextCommand(d->cline);
         }
@@ -96,6 +96,9 @@
     }
 
     case AtCore::PAUSE:
+        if (d->cline.startsWith(QStringLiteral(";#"))) {
+            nextLine();
+        }
         break;
 
     default:
@@ -126,6 +129,9 @@
     qCDebug(PRINT_THREAD) << "progress:" << QString::number(d->printProgress);
     emit(printProgressChanged(d->printProgress));
     if (d->cline.contains(QChar::fromLatin1(';'))) {
+        if (d->cline.startsWith(QStringLiteral(";#"))) {
+            injectCommand(d->cline);
+        }
         d->cline.resize(d->cline.indexOf(QChar::fromLatin1(';')));
     }
     d->cline = d->cline.simplified();
@@ -150,3 +156,39 @@
         connect(d->core, &AtCore::stateChanged, this, &PrintThread::setState, Qt::QueuedConnection);
     }
 }
+
+void PrintThread::injectCommand(QString command)
+{
+    //remove ;#
+    command.remove(0, 2);
+    command = command.simplified();
+    QStringList cmd = command.split(QLatin1Char(':'));
+    cmd.replace(1, cmd.at(1).simplified());
+
+    qCDebug(PRINT_THREAD) << "attempting to inject " << command;
+
+    if (cmd.at(0).startsWith(QStringLiteral("pause"), Qt::CaseInsensitive)) {
+        d->core->pause(cmd.at(1));
+    } else if (cmd.at(0).startsWith(QStringLiteral("setExtTemp"), Qt::CaseInsensitive)) {
+        QStringList arg = cmd.at(1).split(QStringLiteral(","));
+        bool wait = QString::compare(arg.at(2), QStringLiteral("true"), Qt::CaseInsensitive) == 0;
+        d->core->setExtruderTemp(arg.at(0).toInt(), arg.at(1).toInt(), wait);
+    } else if (cmd.at(0).startsWith(QStringLiteral("setBedTemp:"), Qt::CaseInsensitive)) {
+        QStringList arg = cmd.at(1).split(QStringLiteral(","));
+        bool wait = QString::compare(arg.at(1), QStringLiteral("true"), Qt::CaseInsensitive) == 0;
+        d->core->setBedTemp(arg.at(0).toInt(), wait);
+    } else if (cmd.at(0).startsWith(QStringLiteral("setPrintSpeed"), Qt::CaseInsensitive)) {
+        d->core->setPrinterSpeed(cmd.at(1).toInt());
+    } else if (cmd.at(0).startsWith(QStringLiteral("setFlowRate"), Qt::CaseInsensitive)) {
+        d->core->setFlowRate(cmd.at(1).toInt());
+    } else if (cmd.at(0).startsWith(QStringLiteral("setFanSpeed"), Qt::CaseInsensitive)) {
+        QStringList arg = cmd.at(1).split(QStringLiteral(","));
+        d->core->setFanSpeed(arg.at(0).toInt(), arg.at(1).toInt());
+    } else if (cmd.at(0).startsWith(QStringLiteral("showMessage"), Qt::CaseInsensitive)) {
+        d->core->showMessage(cmd.at(1));
+    } else if (cmd.at(0).startsWith(QStringLiteral("Command"), Qt::CaseInsensitive)) {
+        d->core->pushCommand(cmd.at(1));
+    } else {
+        qCDebug(PRINT_THREAD) << "Attempted to inject unknown command: " << command;
+    }
+}