In my experience recording supine and then stadning makes a huge difference in the readings. Even if you wait 5mins + to take the readings. Below info is from the ithlete founder:
“Experienced athletes tend to have low resting heart rates (anything below 60bpm lying down is known as bradycardia, and many athletes are even lower than that).
The heart rate variability test used by ithlete measures the changes in your heart rate when you breathe in (speeds up ) and out (slows down).
Researchers have found that if your resting HR is very low lying down (45 bpm or less) then the gap between heart beats reaches a maximum value when you breathe out, and saturates or hits the end stops as it were! No problem medically, but it limits the range of measurement and you might miss some changes & further improvements in your daily value.
When you stand up, your nervous system adjusts your heart rate upwards about 10 bpm or so (depends on your height, build etc), and you see the full range of HRV when you breathe.
Researchers also found a slightly better ability to detect overtraining from HRV in the standing position.
So we recommend doing the measurement standing up, but if your resting HR when you are well recovered is in the mid 50s or higher and you are more comfortable doing the test lying down, then I don’t see why that should not be OK. Some recent research studies have done morning HRV tests lying down on moderately fit recreational athletes and had good results.”