There is a command in the control B register, which is called "Force COUNT read synchronization". It seems the counter cannot be read without issuing this command.

For example, this worked for me:

while (TCC0->SYNCBUSY.bit.CTRLB); TCC0->CTRLBSET.bit.CMD = TCC_CTRLBSET_CMD_READSYNC_Val; while (TCC0->SYNCBUSY.bit.CTRLB);  while (TCC0->SYNCBUSY.bit.COUNT); 

After this, the value of the counter can be read from TCC0->COUNT.bit.COUNT. I would assume that the vaule I read was the value it had when I issued the TCC0->CTRLBSET.bit.CMD = TCC_CTRLBSET_CMD_READSYNC_Val; command.

More info can be found in this (yet another) Arduino forum topic: https://forum.arduino.cc/index.php?topic=396804.30

_{It seems the Arduino forums are not as well organized regarding duplicate questions as SE.}

There is a command in the Control B register of the TCC peripherals,

• READSYNC – Force a read synchronization of COUNT

The value of the COUNT register is not valid until this command is issued and fully executed.

Sample code, tested on a SAMD21E17A device:

// Step 1: Issue READYSYNC command TCC0->CTRLBSET.reg = TCC_CTRLBSET_CMD_READSYNC;  // Step 2: Wait until the command is fully executed while (TCC0->SYNCBUSY.bit.CTRLB); // or while (TCC0->SYNCBUSY.reg);   // Step 3: Now we can read the value of the COUNT register int count = TCC0->COUNT.reg; 

The resulting value of the variable count corresponds to the value of the counter when the READSYNC command was actually executed.

For additional information, check chapter 31 of the SAM D21/DA1 Family datasheet