diff --git a/arch/arm/boot/dts/omap5-board-common.dtsi b/arch/arm/boot/dts/omap5-board-common.dtsi
index bc853ebeda22..61a06f6add3c 100644
--- a/arch/arm/boot/dts/omap5-board-common.dtsi
+++ b/arch/arm/boot/dts/omap5-board-common.dtsi
@@ -317,7 +317,8 @@
 
 	palmas_sys_nirq_pins: pinmux_palmas_sys_nirq_pins {
 		pinctrl-single,pins = <
-			OMAP5_IOPAD(0x068, PIN_INPUT_PULLUP | MUX_MODE0) /* sys_nirq1 */
+			/* sys_nirq1 is pulled down as the SoC is inverting it for GIC */
+			OMAP5_IOPAD(0x068, PIN_INPUT_PULLUP | MUX_MODE0)
 		>;
 	};
 
@@ -385,7 +386,8 @@
 
 	palmas: palmas@48 {
 		compatible = "ti,palmas";
-		interrupts = <GIC_SPI 7 IRQ_TYPE_NONE>; /* IRQ_SYS_1N */
+		/* sys_nirq/ext_sys_irq pins get inverted at mpuss wakeupgen */
+		interrupts = <GIC_SPI 7 IRQ_TYPE_LEVEL_LOW>;
 		reg = <0x48>;
 		interrupt-controller;
 		#interrupt-cells = <2>;
@@ -651,7 +653,8 @@
 		pinctrl-names = "default";
 		pinctrl-0 = <&twl6040_pins>;
 
-		interrupts = <GIC_SPI 119 IRQ_TYPE_NONE>; /* IRQ_SYS_2N cascaded to gic */
+		/* sys_nirq/ext_sys_irq pins get inverted at mpuss wakeupgen */
+		interrupts = <GIC_SPI 119 IRQ_TYPE_LEVEL_LOW>;
 
 		/* audpwron gpio defined in the board specific dts */
 
diff --git a/arch/arm/boot/dts/omap5-cm-t54.dts b/arch/arm/boot/dts/omap5-cm-t54.dts
index 5e21fb430a65..e78d3718f145 100644
--- a/arch/arm/boot/dts/omap5-cm-t54.dts
+++ b/arch/arm/boot/dts/omap5-cm-t54.dts
@@ -181,6 +181,13 @@
 			OMAP5_IOPAD(0x0042, PIN_INPUT_PULLDOWN | MUX_MODE6)  /* llib_wakereqin.gpio1_wk15 */
 		>;
 	};
+
+	palmas_sys_nirq_pins: pinmux_palmas_sys_nirq_pins {
+		pinctrl-single,pins = <
+			/* sys_nirq1 is pulled down as the SoC is inverting it for GIC */
+			OMAP5_IOPAD(0x068, PIN_INPUT_PULLUP | MUX_MODE0)
+		>;
+	};
 };
 
 &omap5_pmx_core {
@@ -414,8 +421,11 @@
 
 	palmas: palmas@48 {
 		compatible = "ti,palmas";
-		interrupts = <GIC_SPI 7 IRQ_TYPE_NONE>; /* IRQ_SYS_1N */
 		reg = <0x48>;
+		pinctrl-0 = <&palmas_sys_nirq_pins>;
+		pinctrl-names = "default";
+		/* sys_nirq/ext_sys_irq pins get inverted at mpuss wakeupgen */
+		interrupts = <GIC_SPI 7 IRQ_TYPE_LEVEL_LOW>;
 		interrupt-controller;
 		#interrupt-cells = <2>;
 		ti,system-power-controller;
diff --git a/arch/arm/mach-omap2/omap-wakeupgen.c b/arch/arm/mach-omap2/omap-wakeupgen.c
index fc5fb776a710..17558be4bf0a 100644
--- a/arch/arm/mach-omap2/omap-wakeupgen.c
+++ b/arch/arm/mach-omap2/omap-wakeupgen.c
@@ -50,6 +50,9 @@
 #define OMAP4_NR_BANKS		4
 #define OMAP4_NR_IRQS		128
 
+#define SYS_NIRQ1_EXT_SYS_IRQ_1	7
+#define SYS_NIRQ2_EXT_SYS_IRQ_2	119
+
 static void __iomem *wakeupgen_base;
 static void __iomem *sar_base;
 static DEFINE_RAW_SPINLOCK(wakeupgen_lock);
@@ -153,6 +156,37 @@ static void wakeupgen_unmask(struct irq_data *d)
 	irq_chip_unmask_parent(d);
 }
 
+/*
+ * The sys_nirq pins bypass peripheral modules and are wired directly
+ * to MPUSS wakeupgen. They get automatically inverted for GIC.
+ */
+static int wakeupgen_irq_set_type(struct irq_data *d, unsigned int type)
+{
+	bool inverted = false;
+
+	switch (type) {
+	case IRQ_TYPE_LEVEL_LOW:
+		type &= ~IRQ_TYPE_LEVEL_MASK;
+		type |= IRQ_TYPE_LEVEL_HIGH;
+		inverted = true;
+		break;
+	case IRQ_TYPE_EDGE_FALLING:
+		type &= ~IRQ_TYPE_EDGE_BOTH;
+		type |= IRQ_TYPE_EDGE_RISING;
+		inverted = true;
+		break;
+	default:
+		break;
+	}
+
+	if (inverted && d->hwirq != SYS_NIRQ1_EXT_SYS_IRQ_1 &&
+	    d->hwirq != SYS_NIRQ2_EXT_SYS_IRQ_2)
+		pr_warn("wakeupgen: irq%li polarity inverted in dts\n",
+			d->hwirq);
+
+	return irq_chip_set_type_parent(d, type);
+}
+
 #ifdef CONFIG_HOTPLUG_CPU
 static DEFINE_PER_CPU(u32 [MAX_NR_REG_BANKS], irqmasks);
 
@@ -446,7 +480,7 @@ static struct irq_chip wakeupgen_chip = {
 	.irq_mask		= wakeupgen_mask,
 	.irq_unmask		= wakeupgen_unmask,
 	.irq_retrigger		= irq_chip_retrigger_hierarchy,
-	.irq_set_type		= irq_chip_set_type_parent,
+	.irq_set_type		= wakeupgen_irq_set_type,
 	.flags			= IRQCHIP_SKIP_SET_WAKE | IRQCHIP_MASK_ON_SUSPEND,
 #ifdef CONFIG_SMP
 	.irq_set_affinity	= irq_chip_set_affinity_parent,