The Wikipedia article for Baud says that it can be defined as pulses per second. In the case of Manchester Encoding, this results in the baud rate being defined as "clock transitions".
A transition is what occurs when the signaling voltage goes from a low voltage to a high voltage, or vice versa. If you look at this diagram:
You will notice that the Manchester wave always makes a transition from either low to high or high to low when the clock transitions from high to low. The bits are encoded in that transition; a transition from low to high indicates a 1, and a transition from high to low indicates a 0. The low-to-high clock transitions are used to get the Manchester wave in a position where it can make the correct transition for the next bit. As you can see, there are never more than two clock transitions between one Manchester transition and the next; the clock is effectively encoded in the Manchester wave itself.
If the bits were encoded in a single clock transition (i.e. high being 1 and low being 0), then the clock (baud) rate and the bit rate would be the same, but then you would have to run a separate line for the clock. Because Manchester guarantees a transition every
10101010
is imagined. The transitions in this case as seen here are equivalent in both NRZ and Manchester encoding. – Faculty