diff --git a/data/pine64,pinephone-1.0.toml b/data/pine64,pinephone-1.0.toml
index 8b91a88..10dbc1e 100644
--- a/data/pine64,pinephone-1.0.toml
+++ b/data/pine64,pinephone-1.0.toml
@@ -13,11 +13,12 @@ poweron_delay = 100000
 #recovery_timeout = 9
 
 [gpio]
-dtr = 358
-pwrkey = 35
-reset = 68
-apready = 231
-disable = 232
+chips = [ "1c20800.pinctrl", "1f02c00.pinctrl" ]
+dtr = { chip = 1, line = 6 }
+pwrkey = { chip = 0, line = 35 }
+reset = { chip = 0, line = 68 }
+apready = { chip = 0, line = 231 }
+disable = { chip = 0, line = 232 }
 
 [at]
 uart = "/dev/ttyS2"
diff --git a/data/pine64,pinephone-1.1.toml b/data/pine64,pinephone-1.1.toml
index fd09462..9242a91 100644
--- a/data/pine64,pinephone-1.1.toml
+++ b/data/pine64,pinephone-1.1.toml
@@ -13,11 +13,12 @@ poweron_delay = 100000
 #recovery_timeout = 9
 
 [gpio]
-dtr = 358
-pwrkey = 35
-reset = 68
-apready = 231
-disable = 232
+chips = [ "1c20800.pinctrl", "1f02c00.pinctrl" ]
+dtr = { chip = 1, line = 6 }
+pwrkey = { chip = 0, line = 35 }
+reset = { chip = 0, line = 68 }
+apready = { chip = 0, line = 231 }
+disable = { chip = 0, line = 232 }
 
 [at]
 uart = "/dev/ttyS2"
diff --git a/data/pine64,pinephone-1.2.toml b/data/pine64,pinephone-1.2.toml
index 4244bee..3754274 100644
--- a/data/pine64,pinephone-1.2.toml
+++ b/data/pine64,pinephone-1.2.toml
@@ -9,12 +9,13 @@ poweron_delay = 100000
 #recovery_timeout = 9
 
 [gpio]
-dtr = 34
-pwrkey = 35
-reset = 68
-apready = 231
-disable = 232
-status = 233
+chips = [ "1c20800.pinctrl" ]
+dtr = { chip = 0, line = 34 }
+pwrkey = { chip = 0, line = 35 }
+reset = { chip = 0, line = 68 }
+apready = { chip = 0, line = 231 }
+disable = { chip = 0, line = 232 }
+status = { chip = 0, line = 233 }
 
 [at]
 uart = "/dev/ttyS2"
diff --git a/src/gpio.c b/src/gpio.c
index c7cfc53..f9e707c 100644
--- a/src/gpio.c
+++ b/src/gpio.c
@@ -9,9 +9,9 @@
 
 #include <unistd.h>
 
+/* Those defines are used for legacy config files only */
 #define GPIO_CHIP1_LABEL "1c20800.pinctrl"
 #define GPIO_CHIP2_LABEL "1f02c00.pinctrl"
-
 #define MAX_GPIOCHIP_LINES 352
 
 enum {
@@ -101,10 +101,41 @@ int gpio_sequence_sleep(struct EG25Manager *manager)
     return 0;
 }
 
+struct gpiod_line *gpio_get_output_line(struct EG25Manager *manager, int chip, int line)
+{
+    struct gpiod_line *gpio_line;
+
+    gpio_line = gpiod_chip_get_line(manager->gpiochip[chip], line);
+    if (!gpio_line)
+        return NULL;
+
+    if (gpiod_line_request_output(gpio_line, "eg25manager", 0) < 0) {
+        gpiod_line_release(gpio_line);
+        return NULL;
+    }
+
+    return gpio_line;
+}
+
+struct gpiod_line *gpio_get_input_line(struct EG25Manager *manager, int chip, int line)
+{
+    struct gpiod_line *gpio_line;
+
+    gpio_line = gpiod_chip_get_line(manager->gpiochip[chip], line);
+    if (!gpio_line)
+        return NULL;
+
+    if (gpiod_line_request_input(gpio_line, "eg25manager") < 0) {
+        gpiod_line_release(gpio_line);
+        return NULL;
+    }
+
+    return gpio_line;
+}
+
 int gpio_init(struct EG25Manager *manager, toml_table_t *config[])
 {
-    int i, ret;
-    guint offset, chipidx, gpio_idx;
+    int i;
     toml_table_t *gpio_config[EG25_CONFIG_COUNT];
 
     for (i = 0; i < EG25_CONFIG_COUNT; i++)
@@ -113,65 +144,119 @@ int gpio_init(struct EG25Manager *manager, toml_table_t *config[])
     if (!gpio_config[EG25_CONFIG_SYS])
         g_error("Default config file lacks the 'gpio' section!");
 
-    manager->gpiochip[0] = gpiod_chip_open_by_label(GPIO_CHIP1_LABEL);
-    if (!manager->gpiochip[0]) {
-        g_critical("Unable to open GPIO chip " GPIO_CHIP1_LABEL);
-        return 1;
-    }
+    /* 
+     * The system config could have the `chips` key, but the user one
+     * could still use the old format! In order to avoid problems, we
+     * should use the new format only if:
+     *   - there's no user config file
+        or
+     *   - the user config file contains the `chips` key
+     * Otherwise we might start parsing the system config with the new
+     * format, but error out if user config overrides gpios using the
+     * old format
+     */
+    if (!gpio_config[EG25_CONFIG_USER] || toml_array_in(gpio_config[EG25_CONFIG_USER], "chips"))
+    {
+        int numchips;
+        toml_array_t *chipslist = NULL;
 
-    manager->gpiochip[1] = gpiod_chip_open_by_label(GPIO_CHIP2_LABEL);
-    if (!manager->gpiochip[1]) {
-        g_critical("Unable to open GPIO chip " GPIO_CHIP2_LABEL);
-        return 1;
-    }
+        config_get_array(gpio_config, "chips", &chipslist);
+        numchips = toml_array_nelem(chipslist);
+        if (numchips > 2)
+            g_error("Requesting too many GPIO chips!");
 
-    for (i = 0; i < GPIO_OUT_COUNT; i++) {
-        if (!config_get_uint(gpio_config, gpio_out_names[i], &gpio_idx))
-            g_error("Unable to get config for output GPIO '%s'", gpio_out_names[i]);
-
-        if (gpio_idx < MAX_GPIOCHIP_LINES) {
-            offset = gpio_idx;
-            chipidx = 0;
-        } else {
-            offset = gpio_idx - MAX_GPIOCHIP_LINES;
-            chipidx = 1;
+        for (i = 0; i < numchips; i++) {
+            toml_datum_t data = toml_string_at(chipslist, i);
+            if (!data.ok)
+                continue;
+            manager->gpiochip[i] = gpiod_chip_open_by_label(data.u.s);
         }
 
-        manager->gpio_out[i] = gpiod_chip_get_line(manager->gpiochip[chipidx], offset);
-        if (!manager->gpio_out[i]) {
-            g_error("Unable to get output GPIO %d", i);
+        for (i = 0; i < GPIO_OUT_COUNT; i++) {
+            toml_table_t *table;
+            toml_datum_t chip, line;
+            if (!config_get_table(gpio_config, gpio_out_names[i], &table))
+                g_error("Unable to get config for output GPIO '%s'", gpio_out_names[i]);
+
+            chip = toml_int_in(table, "chip");
+            if (!chip.ok || chip.u.i < 0 || chip.u.i > 2)
+                g_error("Wrong chip ID for output GPIO '%s'", gpio_out_names[i]);
+
+            line = toml_int_in(table, "line");
+            if (!line.ok || line.u.i < 0 || line.u.i > gpiod_chip_num_lines(manager->gpiochip[chip.u.i]))
+                g_error("Wrong chip ID for output GPIO '%s'", gpio_out_names[i]);
+
+            manager->gpio_out[i] = gpio_get_output_line(manager, chip.u.i, line.u.i);
+            if (!manager->gpio_out[i])
+                g_error("Unable to get output GPIO %d", i);
+        }
+
+        for (i = 0; i < GPIO_IN_COUNT; i++) {
+            toml_table_t *table;
+            toml_datum_t chip, line;
+            if (!config_get_table(gpio_config, gpio_in_names[i], &table))
+                g_error("Unable to get config for input GPIO '%s'", gpio_in_names[i]);
+
+            chip = toml_int_in(table, "chip");
+            if (!chip.ok || chip.u.i < 0 || chip.u.i > 2)
+                g_error("Wrong chip ID for input GPIO '%s'", gpio_in_names[i]);
+
+            line = toml_int_in(table, "line");
+            if (!line.ok || line.u.i < 0 || line.u.i > gpiod_chip_num_lines(manager->gpiochip[chip.u.i]))
+                g_error("Wrong chip ID for input GPIO '%s'", gpio_in_names[i]);
+
+            manager->gpio_in[i] = gpio_get_input_line(manager, chip.u.i, line.u.i);
+            if (!manager->gpio_in[i])
+                g_error("Unable to get input GPIO %d", i);
+        }
+    } else {
+        guint offset, chipidx, gpio_idx;
+
+        /* Legacy config file, only used on the OG PinePhone */
+        manager->gpiochip[0] = gpiod_chip_open_by_label(GPIO_CHIP1_LABEL);
+        if (!manager->gpiochip[0]) {
+            g_critical("Unable to open GPIO chip " GPIO_CHIP1_LABEL);
             return 1;
         }
 
-        ret = gpiod_line_request_output(manager->gpio_out[i], "eg25manager", 0);
-        if (ret < 0) {
-            g_error("Unable to request output GPIO %d", i);
+        manager->gpiochip[1] = gpiod_chip_open_by_label(GPIO_CHIP2_LABEL);
+        if (!manager->gpiochip[1]) {
+            g_critical("Unable to open GPIO chip " GPIO_CHIP2_LABEL);
             return 1;
         }
-    }
 
-    for (i = 0; i < GPIO_IN_COUNT; i++) {
-        if (!config_get_uint(gpio_config, gpio_in_names[i], &gpio_idx))
-            continue;
+        for (i = 0; i < GPIO_OUT_COUNT; i++) {
+            if (!config_get_uint(gpio_config, gpio_out_names[i], &gpio_idx))
+                g_error("Unable to get config for output GPIO '%s'", gpio_out_names[i]);
 
-        if (gpio_idx < MAX_GPIOCHIP_LINES) {
-            offset = gpio_idx;
-            chipidx = 0;
-        } else {
-            offset = gpio_idx - MAX_GPIOCHIP_LINES;
-            chipidx = 1;
+            if (gpio_idx < MAX_GPIOCHIP_LINES) {
+                offset = gpio_idx;
+                chipidx = 0;
+            } else {
+                offset = gpio_idx - MAX_GPIOCHIP_LINES;
+                chipidx = 1;
+            }
+
+            manager->gpio_out[i] = gpio_get_input_line(manager, chipidx, offset);
+            if (!manager->gpio_out[i])
+                g_error("Unable to get output GPIO %d", i);
         }
 
-        manager->gpio_in[i] = gpiod_chip_get_line(manager->gpiochip[chipidx], offset);
-        if (!manager->gpio_in[i]) {
-            g_warning("Unable to get input GPIO %d", i);
-            continue;
-        }
+        for (i = 0; i < GPIO_IN_COUNT; i++) {
+            if (!config_get_uint(gpio_config, gpio_in_names[i], &gpio_idx))
+                continue;
 
-        ret = gpiod_line_request_input(manager->gpio_in[i], "eg25manager");
-        if (ret < 0) {
-            g_warning("Unable to request input GPIO %d", i);
-            manager->gpio_in[i] = NULL;
+            if (gpio_idx < MAX_GPIOCHIP_LINES) {
+                offset = gpio_idx;
+                chipidx = 0;
+            } else {
+                offset = gpio_idx - MAX_GPIOCHIP_LINES;
+                chipidx = 1;
+            }
+
+            manager->gpio_in[i] = gpio_get_input_line(manager, chipidx, offset);
+            if (!manager->gpio_in[i])
+                g_error("Unable to get input GPIO %d", i);
         }
     }