diff --git a/test/fpga_manual_test.sh b/test/fpga_manual_test.sh
index 64581b1..48acb5d 100755
--- a/test/fpga_manual_test.sh
+++ b/test/fpga_manual_test.sh
@@ -3,51 +3,109 @@
 # Licensed under the Apache License, Version 2.0, see LICENSE for details.
 # SPDX-License-Identifier: Apache-2.0
 set -e
-USAGE="Usage: ./test/fpga_manual_test.sh <UART PORT ATTACHED>.
-Example : ./test/fpga_manual_test.sh /dev/ttyUSB0"
 
-if [ $# == 0 ] ; then
+function usage() {
+    cat << USAGE
+Usage: ./test/fpga_manual_test.sh -u <UART PORT ATTACHED> -n -p.
+-n Controls whether a new fpga bitfile is built
+-p Controls whether the existing bitfile at build/lowrisc_systems_top_earlgrey_nexysvideo_0.1
+is programmed.
+
+The following command builds the fpga, programs it onto the device and begins testing
+./test/fpga_manual_test.sh -u /dev/ttyUSB0 -n -p
+
+The following command assumes there exists a bitfile already, programs it and begins testing
+./test/fpga_manual_test.sh -u /dev/ttyUSB0 -p
+
+The following command assumes the bitfile is already programmed and begins testing
+./test/fpga_manual_test.sh -u /dev/ttyUSB0
+
+USAGE
+}
+
+FPGA_UART=
+BUILD_FPGA=0
+PROGRAM_FPGA=0
+while getopts ':pnu:' opt; do
+  case "${opt}" in
+    u) FPGA_UART=$OPTARG;;
+    n) BUILD_FPGA=1;;
+    p) PROGRAM_FPGA=1;;
+    ?) usage && exit 1;;
+    *) usage
+       error "Unexpected option ${opt}"
+       ;;
+  esac
+done
+
+# Double check a device has been specified
+if [ -z "$FPGA_UART" ] ; then
   echo "Please make sure to pass FPGA's UART port as an argument to the script."
-  echo -e "$USAGE"
   echo "To find out which ttyUSB to use exactly, unplug/plug UART cable and find the last entry in dmesg"
+  echo "Use -h for more usage details"
   exit 1;
 fi
 
-FPGA_UART="$1"
 
-readonly TEST_TARGETS=("flash_ctrl"
-  "hmac"
-  "rv_timer"
+readonly TEST_TARGETS=("flash_ctrl/flash_test.bin"
+  "hmac/sha256_test.bin"
+  "rv_timer/rv_timer_test.bin"
 )
 
-echo "Compiling ROM."
-make -C sw SW_DIR=boot_rom clean all
+BUILD_TARGET=${PWD}/build-fpga
+./meson_init.sh -f
 
-echo "Building FPGA."
-fusesoc --cores-root . build lowrisc:systems:top_earlgrey_nexysvideo
+if [ ${BUILD_FPGA} -eq 1 ] ; then
+  echo "Compiling ROM - this is needed in order for the build step below to correctly infer ROM"
+  ninja -C ${BUILD_TARGET} sw/device/boot_rom/boot_rom.vmem
 
-echo "Splice FPGA."
-util/fpga/splice_nexysvideo.sh
+  echo "Building FPGA."
+  fusesoc --cores-root . build lowrisc:systems:top_earlgrey_nexysvideo \
+  --ROM_INIT_FILE=${BUILD_TARGET}/sw/device/boot_rom/boot_rom.vmem
+fi
 
-echo "Program FPGA."
-fusesoc --cores-root . pgm lowrisc:systems:top_earlgrey_nexysvideo:0.1
+if [ ${PROGRAM_FPGA} -eq 1 ] ; then
+  echo "Splice latest boot ROM and program FPGA."
+  util/fpga/splice_nexysvideo.sh
+  fusesoc --cores-root . pgm lowrisc:systems:top_earlgrey_nexysvideo
+fi
 
 echo "Build spiflash tool."
-make -C sw/host/spiflash clean all
+ninja -C ${BUILD_TARGET} sw/host/spiflash/spiflash
 
 for target in "${TEST_TARGETS[@]}"; do
     echo "Building ${target} binaries."
-    make -C sw SW_DIR=tests/${target} SW_BUILD_DIR=${target}_out clean all
+
+    ninja -C ${BUILD_TARGET} sw/device/tests/${target}/
 done
 
-# Eventually this step should be replaced by PyTest
-# How the test results will be looked at manually
-# To observe results: use
-# miniterm.py /dev/ttyUSBx 230400
-# To find out which ttyUSB to use exactly, unplug/plug UART cable and find
-# the last entry in dmesg
+FAIL_TARGETS=()
+
+# Invoke self contained tests
+
+set +e
 for target in "${TEST_TARGETS[@]}"; do
-    echo "Flashing ${target}_out/sw.bin onto FPGA for tests."
-    ./sw/host/spiflash/spiflash --input=sw/${target}_out/sw.bin
-    sleep 5
+    echo "Flashing binaries onto FPGA for tests."
+    pytest -s -v test/systemtest/functional_fpga_test.py \
+      --test_bin ${BUILD_TARGET}/sw/device/tests/"${target}" \
+      --fpga_uart ${FPGA_UART} \
+      --spiflash sw/host/spiflash/spiflash
+
+    if [[ $? == 1 ]]; then
+      FAIL_TARGETS=("${FAIL_TARGETS[@]}" "${target}")
+    fi
+
 done
+
+if [ ${#FAIL_TARGETS[@]} -eq 0 ]; then
+  echo "TESTS PASS!"
+else
+  echo
+  echo "Failing targets:"
+  for target in "${FAIL_TARGETS[@]}"; do
+    echo "* ${target}"
+  done
+  echo
+  echo "TESTS FAILED!"
+  exit 1
+fi