When Moshe went into the Tent of Meeting to speak with Him, he would hear the Voice addressing him from above the cover that was on top of the Ark of the Pact between the two keruvim; thus He spoke to him.
Chabad.org — English translation + Rashi
Torah Temimah on Numbers 7:89 (note on מדבר אליו): Yoma 4b — “מדבר לו” was not said, but “מדבר אליו,” teaching that Moshe heard and all Israel did not hear.
Sefaria — Yoma 4b · E-Daf — Yoma 4b
English: They raised an objection: “a voice to him,” “a voice to him” — Moshe heard and all Israel did not hear! There is no difficulty: this [case] is at Sinai, and that [case] is in the Tent of Meeting.
Precise wording — “אליו” limits the audience of the divine voice to the one addressed.
In the Ohel Moed the voice was directed to Moshe alone; the verse’s “מדבר אליו” marks that exclusivity, in contrast to the public revelation at Sinai.