Kim Zolciakhas temporarily lost primary custody of the kids she shares with Kroy Biermann … the latest twist in their messy legal battle, TMZ has learned.

A judge just ruled on Kroy’s emergency motion and gave him primary physical custody of the kids.  The ‘Real Housewives of Atlanta’ alum will have limited parenting time with their 4 minor children every other weekend.

Kim and Kroy will continue to share joint legal custody of the children, but Kroy has final decision-making authority regarding educational, non-emergency medical, and religious decisions.

This isn’t the first time … Kim’s custody was also limited last month, only to get reinstated after she completed court-ordered therapy.

Kroy has been pushing hard to keep the kids away from her … filing a motion last week accusing Kim of neglect and claiming she’s “more selfishly concerned with her own image and her work options” than their children’s well-being.

The ex-NFL player argued all 4 should be under one roof … calling Kim “unstable and unfit” and requesting an emergency hearing to change custody immediately.

Kim tells TMZ … the April 29 decision by a senior (retired) judge is only temporary, pending a full hearing once they return to court. She claims the order stemmed from what she describes as an emergency motion filed by Kroy, aimed at getting the case in front of a senior judge rather than their assigned judge — who, she says, has previously denied his requests for immediate hearings despite multiple filings she calls false.”