I have Bluetooth speaker which has microphone in it, when I use it with iPhone and my PC, the microphone works fine. Now I connected it to Raspbian on Raspberry PI 3 B via inbuilt bluetooth, speaker is working but OS is not recognizing microphone. I tried googling for this issue, but no option worked, I am getting only one option in alsamixer. I tried installing bluetooth audio packages also.
I found a solution here: http://youness.net/raspberry-pi/bluetooth-headset-raspberry-pi-3-ad2p-hsp
Basically, Raspberry Pi uses Broadcom BCM43438 “combo” shipset for Wi-Fi and Bluetooth, and there is some problem with the chipset/driver/firmware. The solution entails installing additional drivers for bluetooth support, using an external usb dongle for bluetooth connectivity, disabling the onboard bluetooth transmitter, and installing the correct drivers for the dongle.
I'd recommend viewing the solution from the link directly instead of having me copy-paste it for you, since it will be kept up to date with the authors research and solutions, and because it is a very long post.
Hope this helps!