NBC went almost all color in the 1965-66 season, with the exception of “Convoy (because of black and white stock footage) and I Dream of Jeannie (due to the cost of expensive special effects)” (source). As such, there was never any danger Trek was going to be in B&W so long as it was on NBC.
Incidentally, the whole network went all color 53 years ago today, on my 3rd birthday!
Incidentally, the whole network went all color 53 years ago today, on my 3rd birthday!