diff --git a/libraries/AP_HAL_Linux/GPIO_BBB.cpp b/libraries/AP_HAL_Linux/GPIO_BBB.cpp
index da4b64261f..69c2c222ee 100644
--- a/libraries/AP_HAL_Linux/GPIO_BBB.cpp
+++ b/libraries/AP_HAL_Linux/GPIO_BBB.cpp
@@ -29,20 +29,6 @@ void GPIO_BBB::init()
 {
 #if LINUX_GPIO_NUM_BANKS == 4
     int mem_fd;
-    // Enable all GPIO banks
-    // Without this, access to deactivated banks (i.e. those with no clock source set up) will (logically) fail with SIGBUS
-    // Idea taken from https://groups.google.com/forum/#!msg/beagleboard/OYFp4EXawiI/Mq6s3sg14HoJ
-
-    uint8_t bank_enable[3] = { 5, 65, 105 };
-    int export_fd = open("/sys/class/gpio/export", O_WRONLY | O_CLOEXEC);
-    if (export_fd == -1) {
-        AP_HAL::panic("unable to open /sys/class/gpio/export");
-    }
-    for (uint8_t i=0; i<3; i++) {
-        dprintf(export_fd, "%u\n", (unsigned)bank_enable[i]);
-    }
-    close(export_fd);
-
 
     /* open /dev/mem */
     if ((mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC)) < 0) {
@@ -50,6 +36,22 @@ void GPIO_BBB::init()
             exit (-1);
     }
 
+    /*
+    Enable all GPIO clocks
+    Without this, access to deactivated banks (i.e. those with no clock source set up) will (logically) fail with SIGBUS
+     */
+    volatile unsigned *cm_per = (volatile unsigned *)mmap(0, CM_PER_BASE_SIZE, PROT_READ|PROT_WRITE,
+                                MAP_SHARED, mem_fd, CM_PER_BASE);
+    if ((char *)cm_per == MAP_FAILED) {
+        AP_HAL::panic("unable to map CM_PER registers");
+    }
+    off_t cm_offsets[LINUX_GPIO_NUM_BANKS-1] = { CM_PER_GPIO1_CLKCTRL, CM_PER_GPIO2_CLKCTRL, CM_PER_GPIO3_CLKCTRL };
+    for (uint8_t i=0; i<LINUX_GPIO_NUM_BANKS-1; i++) {
+        unsigned reg_value = *(cm_per + cm_offsets[i]);
+        *(cm_per + cm_offsets[i]) = (reg_value & ~0b11) | 0b10;
+    }
+    munmap((void *)cm_per, CM_PER_BASE_SIZE);
+
     /* mmap GPIO */
     off_t offsets[LINUX_GPIO_NUM_BANKS] = { GPIO0_BASE, GPIO1_BASE, GPIO2_BASE, GPIO3_BASE };
     for (uint8_t i=0; i<LINUX_GPIO_NUM_BANKS; i++) {
diff --git a/libraries/AP_HAL_Linux/GPIO_BBB.h b/libraries/AP_HAL_Linux/GPIO_BBB.h
index e6ba3fbbdd..ad50295f44 100644
--- a/libraries/AP_HAL_Linux/GPIO_BBB.h
+++ b/libraries/AP_HAL_Linux/GPIO_BBB.h
@@ -2,7 +2,12 @@
 
 #include "AP_HAL_Linux.h"
 
-#define SYSFS_GPIO_DIR "/sys/class/gpio"
+#define CM_PER_BASE          0x44E00000
+#define CM_PER_GPIO1_CLKCTRL 0x2B
+#define CM_PER_GPIO2_CLKCTRL 0x2C
+#define CM_PER_GPIO3_CLKCTRL 0x2D
+
+#define CM_PER_BASE_SIZE     0x00003FFF
 
 #define GPIO0_BASE 0x44E07000
 #define GPIO1_BASE 0x4804C000