diff --git a/quicklogic/common/cmake/quicklogic_jlink.cmake b/quicklogic/common/cmake/quicklogic_jlink.cmake
index 85254d15de..527c5fd56e 100644
--- a/quicklogic/common/cmake/quicklogic_jlink.cmake
+++ b/quicklogic/common/cmake/quicklogic_jlink.cmake
@@ -66,24 +66,15 @@ function(ADD_JLINK_OUTPUT)
   add_file_target(FILE ${WORK_DIR_REL}/${IOMUX_CONFIG} GENERATED)
 
   # Convert the binary bitstream to a JLINK script
-  set(BIT_AS_JLINK "top.bit.jlink")
-
-  add_custom_command(
-    OUTPUT ${WORK_DIR}/${BIT_AS_JLINK}
-    COMMAND ${PYTHON3} -m quicklogic_fasm.bitstream_to_jlink ${BITSTREAM_LOC} ${WORK_DIR}/${BIT_AS_JLINK}
-    DEPENDS ${BITSTREAM}
-  )
-
-  add_file_target(FILE ${WORK_DIR_REL}/${BIT_AS_JLINK} GENERATED)
-
-  # Concatenate th bitstream JLink script and the IOMUX config JLink script
   set(OUT_JLINK "top.jlink")
   add_custom_command(
     OUTPUT ${WORK_DIR}/${OUT_JLINK}
-    COMMAND cat ${WORK_DIR}/${BIT_AS_JLINK} ${WORK_DIR}/${IOMUX_CONFIG} >${WORK_DIR}/${OUT_JLINK}
-    DEPENDS ${WORK_DIR}/${BIT_AS_JLINK} ${WORK_DIR}/${IOMUX_CONFIG}
+    COMMAND ${PYTHON3} -m quicklogic_fasm.bitstream_to_jlink ${BITSTREAM_LOC} ${WORK_DIR}/${OUT_JLINK}
+    DEPENDS ${BITSTREAM} ${WORK_DIR}/${IOMUX_CONFIG}
   )
 
+  add_file_target(FILE ${WORK_DIR_REL}/${OUT_JLINK} GENERATED)
+
   add_custom_target(${PARENT}_jlink DEPENDS ${WORK_DIR}/${OUT_JLINK})
 
 
diff --git a/quicklogic/common/cmake/quicklogic_openocd.cmake b/quicklogic/common/cmake/quicklogic_openocd.cmake
index d4b83c7bb7..008e35896f 100644
--- a/quicklogic/common/cmake/quicklogic_openocd.cmake
+++ b/quicklogic/common/cmake/quicklogic_openocd.cmake
@@ -66,24 +66,16 @@ function(ADD_OPENOCD_OUTPUT)
   add_file_target(FILE ${WORK_DIR_REL}/${IOMUX_CONFIG} GENERATED)
 
   # Convert the binary bitstream to a OpenOCD script
-  set(BIT_AS_OPENOCD "top.bit.openocd")
-
-  add_custom_command(
-    OUTPUT ${WORK_DIR}/${BIT_AS_OPENOCD}
-    COMMAND ${PYTHON3} -m quicklogic_fasm.bitstream_to_openocd ${BITSTREAM_LOC} ${WORK_DIR}/${BIT_AS_OPENOCD}
-    DEPENDS ${BITSTREAM}
-  )
-
-  add_file_target(FILE ${WORK_DIR_REL}/${BIT_AS_OPENOCD} GENERATED)
-
-  # Concatenate the bitstream OpenOCD script and the IOMUX config OpenOCD script
   set(OUT_OPENOCD "top.openocd")
+
   add_custom_command(
     OUTPUT ${WORK_DIR}/${OUT_OPENOCD}
-    COMMAND head -n -1 ${WORK_DIR}/${BIT_AS_OPENOCD} > ${WORK_DIR}/${OUT_OPENOCD} && cat ${WORK_DIR}/${IOMUX_CONFIG} >> ${WORK_DIR}/${OUT_OPENOCD} && echo '}' >> ${WORK_DIR}/${OUT_OPENOCD}
-    DEPENDS ${WORK_DIR}/${BIT_AS_OPENOCD} ${WORK_DIR}/${IOMUX_CONFIG}
+    COMMAND ${PYTHON3} -m quicklogic_fasm.bitstream_to_openocd ${BITSTREAM_LOC} ${WORK_DIR}/${OUT_OPENOCD}
+    DEPENDS ${BITSTREAM} ${WORK_DIR}/${IOMUX_CONFIG}
   )
 
+  add_file_target(FILE ${WORK_DIR_REL}/${OUT_OPENOCD} GENERATED)
+
   add_custom_target(${PARENT}_openocd DEPENDS ${WORK_DIR}/${OUT_OPENOCD})
 
 endfunction()
diff --git a/quicklogic/pp3/utils/eos_s3_iomux_config.py b/quicklogic/pp3/utils/eos_s3_iomux_config.py
index 3d5faa79bc..0dfc84ebc8 100755
--- a/quicklogic/pp3/utils/eos_s3_iomux_config.py
+++ b/quicklogic/pp3/utils/eos_s3_iomux_config.py
@@ -22,13 +22,57 @@
     "SDIOMUX": ["PB-SDIOMUX", ],
 }
 
-# Default configuration of the IOMUX pad
-PAD_DEFAULT = {
+# Default configuration of the specific IOMUX pads
+PADS_1 = {
+    2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29,
+    30, 31, 32, 33, 35, 37, 40, 41, 42, 43
+}
+PAD_DEFAULTS_1 = {
+    "func_sel": 0,
+    "ctrl_sel": "A0",
+    "mode": "output",
+    "pull": "none",
+    "drive": 4,
+    "slew": "slow",
+    "schmitt": 0
+}
+PADS_2 = {6, 14, 15, 17, 34, 36, 38, 39, 44, 45}
+PAD_DEFAULTS_2 = {
+    "func_sel": 0,
+    "ctrl_sel": "others",
+    "mode": "output",
+    "pull": "none",
+    "drive": 4,
+    "slew": "slow",
+    "schmitt": 0
+}
+PADS_3 = {8, 9, 19, 20}
+PAD_DEFAULTS_3 = {
+    "func_sel": 0,
+    "ctrl_sel": "A0",
+    "mode": "inout",
+    "pull": "down",
+    "drive": 4,
+    "slew": "slow",
+    "schmitt": 0
+}
+PADS_4 = {0, 1}
+PAD_DEFAULTS_4 = {
     "func_sel": 0,
-    "ctrl_sel": 0,
-    "mode": "none",
+    "ctrl_sel": "A0",
+    "mode": "output",
+    "pull": "up",
+    "drive": 4,
+    "slew": "slow",
+    "schmitt": 0
+}
+PADS_5 = {16}
+PAD_DEFAULTS_5 = {
+    "func_sel": 0,
+    "ctrl_sel": "A0",
+    "mode": "inout",
     "pull": "none",
-    "drive": 2,
+    "drive": 4,
     "slew": "slow",
     "schmitt": 0
 }
@@ -53,9 +97,6 @@ def generate_iomux_register_content(config):
         pad = int(pad)
         reg = 0
 
-        # Patch default settings with settings read from the config file
-        pad_cfg = dict(PAD_DEFAULT, **pad_cfg)
-
         func_sel = pad_cfg["func_sel"]
         assert func_sel in [0, 1], func_sel
         reg |= func_sel
@@ -137,6 +178,55 @@ def generate_iomux_register_content(config):
     return iomux_regs
 
 
+def get_pad_no(pad_alias):
+    pad = None
+
+    match = re.match(r"^IO_([0-9]+)$", pad_alias)
+    if match is not None:
+        pad = int(match.group(1))
+
+    if pad is None or pad < 0 or pad >= 46:
+        print("Pad not found or out of range: {}".format(pad))
+        return -1
+
+    return pad
+
+
+def pad_defconfig_lookup(pad):
+    pad_config = None
+
+    if pad in PADS_1:
+        pad_config = PAD_DEFAULTS_1
+    elif pad in PADS_2:
+        pad_config = PAD_DEFAULTS_2
+    elif pad in PADS_3:
+        pad_config = PAD_DEFAULTS_3
+    elif pad in PADS_4:
+        pad_config = PAD_DEFAULTS_4
+    elif pad in PADS_5:
+        pad_config = PAD_DEFAULTS_5
+    else:
+        raise ValueError(
+            "Unknown default IOMUX configuration for pad: {}".format(pad)
+        )
+
+    return pad_config
+
+
+def prepare_default_config(pad_map):
+    config = {"pads": {}}
+
+    # Populate IO config with default configuration for each pad
+    for pin in pad_map.items():
+        pad = get_pad_no(pin[1])
+        if (pad == -1):
+            continue
+
+        config["pads"][str(pad)] = pad_defconfig_lookup(pad)
+
+    return config
+
+
 # =============================================================================
 
 
@@ -179,16 +269,44 @@ def main():
         required=True,
         help='Pin map CSV file'
     )
+    parser.add_argument(
+        "--default-config",
+        action="store_true",
+        help='generate default IOMUX config that will be overlaid by the design'
+    )
 
     parser.add_argument(
         "--output-format",
         default=None,
         type=str,
-        help='Output format of IOMUX commands (openocd/jlink)'
+        help='Output format of IOMUX commands (openocd/jlink/binary)'
     )
 
     args = parser.parse_args()
 
+    pad_map = {}
+    pad_alias_map = {}
+
+    # Read pinmap
+    for pin_map_entry in csv.DictReader(args.map):
+
+        if pin_map_entry['type'] not in IOB_TYPES:
+            continue
+
+        name = pin_map_entry['name']
+        alias = ""
+        if 'alias' in pin_map_entry:
+            alias = pin_map_entry['alias']
+            pad_alias_map[alias] = name
+            pad_map[name] = alias
+        else:
+            pad_map[name] = name
+
+    if (args.default_config):
+        config = prepare_default_config(pad_map)
+    else:
+        config = {"pads": {}}
+
     # Read the requested configurtion from a JSON file
     if args.json is not None:
 
@@ -197,7 +315,17 @@ def main():
             exit(-1)
 
         with open(args.json, "r") as fp:
-            config = json.load(fp)
+            json_config = json.load(fp)
+
+        # Overlay default config
+        for design_pad, pad_config in json_config["pads"].items():
+            if (args.default_config):
+                config["pads"][str(design_pad)] = dict(
+                    config["pads"][str(design_pad)], **pad_config
+                )
+            else:
+                defconfig = pad_defconfig_lookup(int(design_pad))
+                config["pads"][design_pad] = dict(defconfig, **pad_config)
 
     # Generate the config according to the EBLIF netlist and PCF constraints.
     else:
@@ -206,23 +334,6 @@ def main():
             print("Use either '--json' or '--pcf' + '--eblif' options!")
             exit(-1)
 
-        pad_map = {}
-        pad_alias_map = {}
-
-        for pin_map_entry in csv.DictReader(args.map):
-
-            if pin_map_entry['type'] not in IOB_TYPES:
-                continue
-
-            name = pin_map_entry['name']
-            alias = ""
-            if 'alias' in pin_map_entry:
-                alias = pin_map_entry['alias']
-                pad_alias_map[alias] = name
-                pad_map[name] = alias
-            else:
-                pad_map[name] = name
-
         # Read and parse PCF
         with open(args.pcf, "r") as fp:
             pcf = list(parse_simple_pcf(fp))
@@ -231,9 +342,6 @@ def main():
         with open(args.eblif, "r") as fp:
             eblif = parse_blif(fp)
 
-        # Build the config
-        config = {"pads": {}}
-
         eblif_inputs = eblif["inputs"]["args"]
         eblif_outputs = eblif["outputs"]["args"]
 
@@ -261,19 +369,14 @@ def main():
             if pad_name in pad_alias_map:
                 pad_alias = pad_name
 
-            pad = None
-
-            match = re.match(r"^IO_([0-9]+)$", pad_alias)
-            if match is not None:
-                pad = int(match.group(1))
-
-            # Pad not found or out of range
-            if pad is None or pad < 0 or pad >= 46:
+            pad_no = get_pad_no(pad_alias)
+            if (pad_no == -1):
                 continue
 
             # Detect inouts:
             is_inout_in = constraint.net + '_$inp' in eblif_inputs
             is_inout_out = constraint.net + '_$out' in eblif_outputs
+
             if is_inout_in and is_inout_out:
                 pad_config = {
                     "ctrl_sel": "fabric",
@@ -296,7 +399,14 @@ def main():
             else:
                 assert False, (constraint.net, constraint.pad)
 
-            config["pads"][str(pad)] = pad_config
+            # Overlay default config
+            if (args.default_config):
+                config["pads"][str(pad_no)] = dict(
+                    config["pads"][str(pad_no)], **pad_config
+                )
+            else:
+                defconfig = pad_defconfig_lookup(pad_no)
+                config["pads"][str(pad_no)] = dict(defconfig, **pad_config)
 
     # Convert the config to IOMUX register content
     iomux_regs = generate_iomux_register_content(config)