This phrase implies a lack of emotional investment or passion in an activity or task. She's been working as a consultant for years, but her heart is not in it anymore.
Pro Tip 2/3
Effort Indicator
If someone's heart is not in something, it often signals minimal effort or interest in performing the task well. He's playing the piano, but his heart is not in it, so the music lacks feeling.
Pro Tip 3/3
Not Just Disinterest
The phrase can also suggest a desire to be involved in other pursuits or a need for change. Maria helps at the family store but her heart is not in it; she dreams of being an artist.