diff --git a/hardware/mux_rpi/mux_rpi.ino b/hardware/mux_rpi/mux_rpi.ino
index d74841d..7540828 100644
--- a/hardware/mux_rpi/mux_rpi.ino
+++ b/hardware/mux_rpi/mux_rpi.ino
@@ -23,24 +23,39 @@ bool ledState = false;
 void TC5_Handler(void);
 void timerConfigure(int sampleRate);
 
+// General UART configuration struct
+struct {
+  // Whether or not the USB is used for serial communications (stand alone builds)
+  bool Serial = true;
+  // Whether or not the i2c is used for serial communication (_controller builds)
+  bool uartI2C = false;
+
+  // Use the generic uart setup with the rpi
+  bool Serial1 = true;
+  // Use uart0 on the rpi
+  bool rpiUART0 = true;
+  // Use uart5 on the rpi
+  bool rpiUART5 = true;
+} uartConfig;
+
 // Additional serial ports for communication <> RPI
 //     https://learn.adafruit.com/using-atsamd21-sercom-to-add-more-spi-i2c-serial-ports?view=all#creating-a-new-serial
 //     D11 (RX) -- GPIO 8 (TX)
 //     D10 (TX) -- GPIO 10 (RX)
 //     MISO (RX) -- GPIO 32 (TX)
 //     MOSI (TX) -- GPIO 33 (RX)
-
 Uart rpiUART0 (&sercom1, 10, 11, SERCOM_RX_PAD_0, UART_TX_PAD_2);
 Uart rpiUART5 (&sercom4, PIN_SPI_MISO, PIN_SPI_MOSI, SERCOM_RX_PAD_0, UART_TX_PAD_2);
-
 void SERCOM1_Handler() {
   rpiUART0.IrqHandler();
 }
-
 void SERCOM4_Handler() {
   rpiUART5.IrqHandler();
 }
 
+// Misc uart functions (defined after setup/loop)
+void setupUARTs();
+
 // Setup stuff needed for build
 void setup() {
   // Setup board LED
@@ -50,11 +65,8 @@ void setup() {
   timerConfigure(TIMER_MILLIS);
   timerStartCounter();
 
-  // Setup serial ports
-  Serial.begin(115200);
-  Serial1.begin(115200);
-  rpiUART0.begin(115200);
-  rpiUART5.begin(115200);
+  // Setup UARTS
+  setupUARTs();
 
   // Assign SERCOM functionality
   pinPeripheral(10, PIO_SERCOM);
@@ -64,23 +76,58 @@ void setup() {
 // Main function
 int serialIncomingByte;
 void loop() {
-  while (Serial.available()) {
+  while (uartConfig.Serial && Serial.available()) {
     uartBufferOutbound.push(Serial.read());
-    Serial1.write(uartBufferOutbound.last());
-    rpiUART0.write(uartBufferOutbound.last());
-    rpiUART5.write(uartBufferOutbound.last());
+    if (uartConfig.Serial1) {
+      Serial1.write(uartBufferOutbound.last());
+    }
+    if (uartConfig.rpiUART0) {
+      rpiUART0.write(uartBufferOutbound.last());
+    }
+    if (uartConfig.rpiUART5) {
+      rpiUART5.write(uartBufferOutbound.last());
+    }
   }
-  while (Serial1.available()) {
+  while (uartConfig.Serial1 && Serial1.available()) {
     uartBufferInbound.push(Serial1.read());
-    Serial.write(uartBufferInbound.last());
+    if (uartConfig.Serial) {
+      Serial.write(uartBufferInbound.last());
+    }
   }
-  while (rpiUART0.available()) {
+  while (uartConfig.rpiUART0 && rpiUART0.available()) {
     uartBufferInbound.push(rpiUART0.read());
-    Serial.write(uartBufferInbound.last());
+    if (uartConfig.Serial) {
+      Serial.write(uartBufferInbound.last());
+    }
   }
-  while (rpiUART5.available()) {
+  while (uartConfig.rpiUART5 && rpiUART5.available()) {
     uartBufferInbound.push(rpiUART5.read());
-    Serial.write(uartBufferInbound.last());
+    if (uartConfig.Serial) {
+      Serial.write(uartBufferInbound.last());
+    }
+  }
+}
+
+// Method to setup / reset the uarts
+void setupUARTs() {
+  // Close ALL serial ports and re-enable per config (config can change during runtime)
+  Serial.end();
+  Serial1.end();
+  rpiUART0.end();
+  rpiUART5.end();
+
+  // Setup serial ports
+  if (uartConfig.Serial) {
+    Serial.begin(115200);
+  }
+  if (uartConfig.Serial1) {
+    Serial1.begin(115200);
+  }
+  if (uartConfig.rpiUART0) {
+    rpiUART0.begin(115200);
+  }
+  if (uartConfig.rpiUART5) {
+    rpiUART5.begin(115200);
   }
 }