diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..81db34d
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,27 @@
+# Project makefile (depends on firmware/Makefile)
+# ===============================================
+FIRMWARE_DIR = firmware
+
+.PHONY: all clean build firmware firmware-clean firmware-build firmware-flash
+
+
+# Default target (build firmware)
+all: firmware
+
+# Shortcuts
+clean: firmware-clean
+build: firmware-build
+
+
+# Firmware
+# --------
+firmware: firmware-build
+
+firmware-clean:
+	make -C $(FIRMWARE_DIR) clean
+
+firmware-build:
+	make -C $(FIRMWARE_DIR) build
+
+firmware-flash:
+	make -C $(FIRMWARE_DIR) flash
diff --git a/firmware/Makefile b/firmware/Makefile
index ee9c4a0..b04be63 100644
--- a/firmware/Makefile
+++ b/firmware/Makefile
@@ -1,10 +1,10 @@
-################
-# CONFIGURATION
-################
+# Makefile for the EEPROM programmer microcontroller firmware
+# ===========================================================
 
 # Compiler and tools
 CC = avr-gcc
 OBJCOPY = avr-objcopy
+AVRDUDE = avrdude
 
 # Compiler and linker flags
 CFLAGS = -Wall -std=c11 -Os
@@ -14,63 +14,62 @@ LDFLAGS =
 GCC_MCU = atmega16a
 AVRDUDE_PARTNO = m16
 AVRDUDE_PROGRAMMER = usbtiny
+AVRDUDE_CMD = $(AVRDUDE) -p $(AVRDUDE_PARTNO) -c $(AVRDUDE_PROGRAMMER)
 
-# Make target and object files
-TARGET = build/eepprog
-OBJECTS = build/main.o build/uart.o build/eeprom.o build/protocol.o
-HEADERS = src/config.h src/BitIO.h src/uart.h src/eeprom.h src/protocol.h
+# Directories
+SOURCE_DIR = src
+BUILD_DIR = build
+
+# Make targets and object files
+SOURCE_FILES = $(wildcard $(SOURCE_DIR)/*.c)
+HEADER_FILES = $(wildcard $(SOURCE_DIR)/*.h)
+OBJECT_FILES = $(patsubst $(SOURCE_DIR)/%.c,$(BUILD_DIR)/%.o,$(SOURCE_FILES))
+
+TARGET_NAME = eepprog
+TARGET_ELF = $(BUILD_DIR)/$(TARGET_NAME).elf
+TARGET_HEX = $(BUILD_DIR)/$(TARGET_NAME).hex
+
+.PHONY: all clean build flash writeflash readfuse writefuse
 
 # Default target (build hex file)
-all: hex
+all: build
 
 
-################
-# BUILD TARGETS
-################
-
-# Shortcuts for build targets
-hex: $(TARGET).hex
-elf: $(TARGET).elf
-
-# Convert elf binary to ihex format
-$(TARGET).hex: $(TARGET).elf
-	$(OBJCOPY) -O ihex $(TARGET).elf $(TARGET).hex
-
-# Elf binary
-$(TARGET).elf: $(OBJECTS)
-	$(CC) -mmcu=$(GCC_MCU) $(LDFLAGS) -o $(TARGET).elf $(OBJECTS)
-
-# Object files
-build/%.o: src/%.c $(HEADERS)
-	@mkdir -p build/
-	$(CC) -mmcu=$(GCC_MCU) $(CFLAGS) -c -o $@ $<
-
-
-##############
-# PROGRAMMING
-##############
-
-# Program controller
-program: writeflash
-
-writeflash: $(TARGET).hex
-	sudo avrdude -p $(AVRDUDE_PARTNO) -c $(AVRDUDE_PROGRAMMER) -U flash:w:$(TARGET).hex
-
-readfuse:
-	sudo avrdude -p $(AVRDUDE_PARTNO) -c $(AVRDUDE_PROGRAMMER) -U lfuse:r:m -U hfuse:r:m
-
-writefuse:
-	sudo avrdude -p $(AVRDUDE_PARTNO) -c $(AVRDUDE_PROGRAMMER) -U lfuse:w:0xef:m -U hfuse:w:0xd9:m
-
-
-################
-# OTHER TARGETS
-################
+# General
+# -------
 
 # Clean generated files
 clean:
-	rm -f $(OBJECTS) $(TARGET).elf $(TARGET).hex
+	rm -rf $(BUILD_DIR)
 
 
-.PHONY: all hex elf program writeflash clean
+# Build firmware
+# --------------
+build: $(TARGET_HEX)
 
+# Compile C code to object files
+$(BUILD_DIR)/%.o: $(SOURCE_DIR)/%.c $(HEADER_FILES)
+	@mkdir -p $(BUILD_DIR)
+	$(CC) -mmcu=$(GCC_MCU) $(CFLAGS) -c -o $@ $<
+
+# Link object files to ELF binary
+$(TARGET_ELF): $(OBJECT_FILES)
+	$(CC) -mmcu=$(GCC_MCU) $(LDFLAGS) -o $(TARGET_ELF) $(OBJECT_FILES)
+
+# Convert ELF binary to ihex format (which can be flashed to the microcontroller)
+$(TARGET_HEX): $(TARGET_ELF)
+	$(OBJCOPY) -O ihex $(TARGET_ELF) $(TARGET_HEX)
+
+
+# Flash firmware
+# --------------
+flash: writeflash
+
+writeflash: $(TARGET_HEX)
+	$(AVRDUDE_CMD) -U flash:w:$(TARGET_HEX)
+
+readfuse:
+	$(AVRDUDE_CMD) -U lfuse:r:m -U hfuse:r:m
+
+writefuse:
+	$(AVRDUDE_CMD) -U lfuse:w:0xef:m -U hfuse:w:0xd9:m