Image imported from derpibooru 
Original Description:
 
After reading chapter 3 again and seeing the scenes where Applejack flexes and grows her muscles, I reread chapter 2 and seeing the start of AJ’s transformation, I thought that before she transformed into an Amazon, she showed us her musculature. *It seems that her muscles only show when she flexes them.
 
My theory is based on the fact that we observe that she fixes on her nails and not on her muscles, she possibly flexed her muscles when she felt the effect of the formula before starting to grow. In addition to the fact that her clothes remain intact and without tears.