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My project is based around the ATMEGA32u4 microcontroller.

I followed the Arduino Pro Micro schematic to design my own board layout and build a custom PCB, soldered on the components. Then I used the Arduino IDE to successfully upload the Arduino bootloader with SPI.

Currently I can also upload programs to my `32u4 over SPI (using "in-serial programming"). Tested that with Blink.

But I cannot upload programs with the USB, like you would normally be able to do with a Pro Micro. What things should I look for to debug this?

avrdude: Version 6.3, compiled on Jan 17 2017 at 12:00:53 Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/ Copyright (c) 2007-2014 Joerg Wunsch System wide configuration file is "C:\Users\Myname\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino9/etc/avrdude.conf" Using Port : COM12 Using Programmer : avr109 Overriding Baud Rate : 57600 AVR Part : ATmega32U4 Chip Erase delay : 9000 us PAGEL : PD7 BS2 : PA0 RESET disposition : dedicated RETRY pulse : SCK serial program mode : yes parallel program mode : yes Timeout : 200 StabDelay : 100 CmdexeDelay : 25 SyncLoops : 32 ByteDelay : 0 PollIndex : 3 PollValue : 0x53 Memory Detail : Block Poll Page Polled Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- --------- eeprom 65 20 4 0 no 1024 4 0 9000 9000 0x00 0x00 flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00 lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00 hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00 efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00 lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00 calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00 signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00 Programmer Type : butterfly Description : Atmel AppNote AVR109 Boot Loader Connecting to programmer: .avrdude: butterfly_recv(): programmer is not responding
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    When you program the blink sketch using ISP, you overwrite the bootloader!!! Did you set the correct fuses? How did you program the bootloader? Commented May 10, 2018 at 15:53
  • Oh, I did not know that. I used an Arduino UNO as a SPI master to upload the bootloader to my 32u4. After that I uploaded a blink sketch the same way. I will try uploading the bootloader again and then the sketch via USB. Commented May 10, 2018 at 16:19
  • Yes, that worked. Thanks, would have taken me a long time to work that out. I will post a reply. Commented May 10, 2018 at 16:25
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    It’s one of those gotchas. Glad you got it working now. Commented May 10, 2018 at 16:26

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The answer, as kindly pointed out by Gerben, is that ISP program upload overwrites the bootloader.

Only upload the bootloader via ISP, then switch to USB for uploading Arduino sketches.

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