diff --git a/board/keymile/common/common.h b/board/keymile/common/common.h
index f457aa3..aab706e 100644
--- a/board/keymile/common/common.h
+++ b/board/keymile/common/common.h
@@ -131,6 +131,11 @@
 int ethernet_present(void);
 int ivm_read_eeprom(void);
 
+int trigger_fpga_config(void);
+int wait_for_fpga_config(void);
+int fpga_reset(void);
+int toggle_eeprom_spi_bus(void);
+
 int set_km_env(void);
 int fdt_set_node_and_value(void *blob,
 			char *nodename,
diff --git a/board/keymile/km_arm/Makefile b/board/keymile/km_arm/Makefile
index aa51255..13d485a 100644
--- a/board/keymile/km_arm/Makefile
+++ b/board/keymile/km_arm/Makefile
@@ -31,6 +31,10 @@
 
 COBJS	:= $(BOARD).o ../common/common.o ../common/ivm.o
 
+ifdef CONFIG_KM_FPGA_CONFIG
+COBJS	+= fpga_config.o
+endif
+
 SRCS	:= $(SOBJS:.o=.S) $(COBJS:.o=.c)
 OBJS	:= $(addprefix $(obj),$(COBJS))
 SOBJS	:= $(addprefix $(obj),$(SOBJS))
diff --git a/board/keymile/km_arm/fpga_config.c b/board/keymile/km_arm/fpga_config.c
new file mode 100644
index 0000000..4356b9a
--- /dev/null
+++ b/board/keymile/km_arm/fpga_config.c
@@ -0,0 +1,212 @@
+/*
+ * (C) Copyright 2012
+ * Valentin Lontgchamp, Keymile AG, valentin.longchamp@keymile.com
+ *
+ * See file CREDITS for list of people who contributed to this
+ * project.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.	 See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301 USA
+ */
+
+#include <common.h>
+#include <i2c.h>
+#include <asm/errno.h>
+
+/* GPIO Pin from kirkwood connected to PROGRAM_B pin of the xilinx FPGA */
+#define KM_XLX_PROGRAM_B_PIN    39
+
+#define BOCO_ADDR	0x10
+
+#define ID_REG		0x00
+#define BOCO2_ID	0x5b
+
+static int check_boco2(void)
+{
+	int ret;
+	u8 id;
+
+	ret = i2c_read(BOCO_ADDR, ID_REG, 1, &id, 1);
+	if (ret) {
+		printf("%s: error reading the BOCO id !!\n", __func__);
+		return ret;
+	}
+
+	return (id == BOCO2_ID);
+}
+
+static int boco_clear_bits(u8 reg, u8 flags)
+{
+	int ret;
+	u8 regval;
+
+	/* give access to the EEPROM from FPGA */
+	ret = i2c_read(BOCO_ADDR, reg, 1, &regval, 1);
+	if (ret) {
+		printf("%s: error reading the BOCO @%#x !!\n",
+			__func__, reg);
+		return ret;
+	}
+	regval &= ~flags;
+	ret = i2c_write(BOCO_ADDR, reg, 1, &regval, 1);
+	if (ret) {
+		printf("%s: error writing the BOCO @%#x !!\n",
+			__func__, reg);
+		return ret;
+	}
+
+	return 0;
+}
+
+static int boco_set_bits(u8 reg, u8 flags)
+{
+	int ret;
+	u8 regval;
+
+	/* give access to the EEPROM from FPGA */
+	ret = i2c_read(BOCO_ADDR, reg, 1, &regval, 1);
+	if (ret) {
+		printf("%s: error reading the BOCO @%#x !!\n",
+			__func__, reg);
+		return ret;
+	}
+	regval |= flags;
+	ret = i2c_write(BOCO_ADDR, reg, 1, &regval, 1);
+	if (ret) {
+		printf("%s: error writing the BOCO @%#x !!\n",
+			__func__, reg);
+		return ret;
+	}
+
+	return 0;
+}
+
+#define SPI_REG		0x06
+#define CFG_EEPROM	0x02
+#define FPGA_PROG	0x04
+#define FPGA_DONE	0x20
+
+int trigger_fpga_config(void)
+{
+	int ret = 0;
+
+	if (check_boco2()) {
+		/* we have a BOCO2, this has to be triggered here */
+
+		/* make sure the FPGA_can access the EEPROM */
+		ret = boco_clear_bits(SPI_REG, CFG_EEPROM);
+		if (ret)
+			return ret;
+
+		/* trigger the config start */
+		ret = boco_clear_bits(SPI_REG, FPGA_PROG);
+		if (ret)
+			return ret;
+
+		/* small delay for the pulse */
+		udelay(10);
+
+		/* up signal for pulse end */
+		ret = boco_set_bits(SPI_REG, FPGA_PROG);
+		if (ret)
+			return ret;
+
+	} else {
+		/* we do it the old way, with the gpio pin */
+		kw_gpio_set_valid(KM_XLX_PROGRAM_B_PIN, 1);
+		kw_gpio_direction_output(KM_XLX_PROGRAM_B_PIN, 0);
+		/* small delay for the pulse */
+		udelay(10);
+		kw_gpio_direction_input(KM_XLX_PROGRAM_B_PIN);
+	}
+
+	return 0;
+}
+
+int wait_for_fpga_config(void)
+{
+	int ret = 0;
+	u8 spictrl;
+	u32 timeout = 20000;
+
+	if (!check_boco2()) {
+		/* we do not have BOCO2, this is not really used */
+		return 0;
+	}
+
+	printf("PCIe FPGA config:");
+	do {
+		ret = i2c_read(BOCO_ADDR, SPI_REG, 1, &spictrl, 1);
+		if (ret) {
+			printf("%s: error reading the BOCO spictrl !!\n",
+				__func__);
+			return ret;
+		}
+		if (timeout-- == 0) {
+			printf(" FPGA_DONE timeout\n");
+			return -EFAULT;
+		}
+		udelay(10);
+	} while (!(spictrl & FPGA_DONE));
+
+	printf(" done\n");
+
+	return 0;
+}
+
+#define PRST1		0x4
+#define BRIDGE_RST	0x4
+
+int fpga_reset(void)
+{
+	int ret = 0;
+
+	if (!check_boco2()) {
+		/* we do not have BOCO2, this is not really used */
+		return 0;
+	}
+
+	ret = boco_clear_bits(PRST1, BRIDGE_RST);
+	if (ret)
+		return ret;
+
+	/* small delay for the pulse */
+	udelay(10);
+
+	ret = boco_set_bits(PRST1, BRIDGE_RST);
+	if (ret)
+		return ret;
+
+	return 0;
+}
+
+/* the FPGA was configured, we configure the BOCO2 so that the EEPROM
+ * is available from the Bobcat SPI bus */
+int toggle_eeprom_spi_bus(void)
+{
+	int ret = 0;
+
+	if (!check_boco2()) {
+		/* we do not have BOCO2, this is not really used */
+		return 0;
+	}
+
+	ret = boco_set_bits(SPI_REG, CFG_EEPROM);
+	if (ret)
+		return ret;
+
+	return 0;
+}
+
diff --git a/board/keymile/km_arm/km_arm.c b/board/keymile/km_arm/km_arm.c
index daab27b..c8da823 100644
--- a/board/keymile/km_arm/km_arm.c
+++ b/board/keymile/km_arm/km_arm.c
@@ -268,12 +268,6 @@
 	kw_gpio_set_valid(KM_KIRKWOOD_ENV_WP, 38);
 	kw_gpio_direction_output(KM_KIRKWOOD_ENV_WP, 1);
 #endif
-#if defined(CONFIG_KM_RECONFIG_XLX)
-	/* trigger the reconfiguration of the xilinx fpga */
-	kw_gpio_set_valid(KM_XLX_PROGRAM_B_PIN, 1);
-	kw_gpio_direction_output(KM_XLX_PROGRAM_B_PIN, 0);
-	kw_gpio_direction_input(KM_XLX_PROGRAM_B_PIN);
-#endif
 	return 0;
 }
 
@@ -282,6 +276,21 @@
 	/* address of boot parameters */
 	gd->bd->bi_boot_params = kw_sdram_bar(0) + 0x100;
 
+#if defined(CONFIG_KM_FPGA_CONFIG)
+	trigger_fpga_config();
+#endif
+
+	return 0;
+}
+
+int board_late_init(void)
+{
+#if defined(CONFIG_KM_FPGA_CONFIG)
+	wait_for_fpga_config();
+	fpga_reset();
+	toggle_eeprom_spi_bus();
+#endif
+
 	return 0;
 }
 
diff --git a/boards.cfg b/boards.cfg
index db7902f..26c0a99 100644
--- a/boards.cfg
+++ b/boards.cfg
@@ -141,7 +141,7 @@
 lschlv2                      arm         arm926ejs   lsxl                buffalo        kirkwood    lsxl:LSCHLV2
 lsxhl                        arm         arm926ejs   lsxl                buffalo        kirkwood    lsxl:LSXHL
 km_kirkwood                  arm         arm926ejs   km_arm              keymile        kirkwood    km_kirkwood:KM_KIRKWOOD,KM_DISABLE_PCI
-km_kirkwood_pci              arm         arm926ejs   km_arm              keymile        kirkwood    km_kirkwood:KM_KIRKWOOD_PCI,KM_RECONFIG_XLX
+km_kirkwood_pci              arm         arm926ejs   km_arm              keymile        kirkwood    km_kirkwood:KM_KIRKWOOD_PCI,KM_FPGA_CONFIG
 kmnusa                       arm         arm926ejs   km_arm              keymile        kirkwood    km_kirkwood:KM_NUSA
 mgcoge3un                    arm         arm926ejs   km_arm              keymile        kirkwood    km_kirkwood:KM_MGCOGE3UN
 kmcoge5un                    arm         arm926ejs   km_arm              keymile        kirkwood    km_kirkwood:KM_COGE5UN
diff --git a/include/configs/km/km_arm.h b/include/configs/km/km_arm.h
index 60e2450..1a5f04b 100644
--- a/include/configs/km/km_arm.h
+++ b/include/configs/km/km_arm.h
@@ -313,4 +313,7 @@
 #define CONFIG_POST_EXTERNAL_WORD_FUNCS
 #define CONFIG_CMD_DIAG
 
+/* we do the whole PCIe FPGA config stuff here */
+#define	BOARD_LATE_INIT
+
 #endif /* _CONFIG_KM_ARM_H */
diff --git a/include/configs/km_kirkwood.h b/include/configs/km_kirkwood.h
index 44a3e7a6..0a61b7d 100644
--- a/include/configs/km_kirkwood.h
+++ b/include/configs/km_kirkwood.h
@@ -162,10 +162,12 @@
 	MVGBE_SET_MII_SPEED_TO_100)
 #endif
 
-/* GPIO Pin from kirkwood connected to PROGRAM_B pin of the xilinx FPGA */
-#define KM_XLX_PROGRAM_B_PIN    39
-
 #ifdef CONFIG_KM_DISABLE_PCI
 #undef  CONFIG_KIRKWOOD_PCIE_INIT
 #endif
+
+#ifndef CONFIG_KM_FPGA_CONFIG
+#undef  BOARD_LATE_INIT
+#endif
+
 #endif /* _CONFIG_KM_KIRKWOOD */