diff --git a/src/atsam/gpio.c b/src/atsam/gpio.c
index 2af2bfc0..f3ad95ac 100644
--- a/src/atsam/gpio.c
+++ b/src/atsam/gpio.c
@@ -60,6 +60,9 @@ set_pull_up(Pio *regs, uint32_t bit, int32_t pull_up)
         regs->PIO_PUDR = bit;
         regs->PIO_PPDDR = bit;
     }
+    // Check if this pin is a "system IO pin" and disable if so
+    if (regs == PIOB && (bit & 0x1cf0))
+        MATRIX->CCFG_SYSIO |= bit;
 #endif
 }