It’s a popular misconception! Although the amount of calcium in urine increases slightly after drinking coffee, the net effect on calcium levels in the body is negligible.
This is because calcium excretion from the body decreases later during the day. Recent evidence has shown that drinking coffee in moderation has no negative effect on bone health!
And of course, strong healthy bones are a result of adequate calcium and vitamin D intake as well as regular weight-bearing exercise.
Come to think of it, if preparing your coffee with milk will encourage you to drink your glass of milk, then it actually helps you meet your calcium needs for healthier bones.