The coupling between them is great, the light coming out is barely visible because the light goes through a liquid sample where most of it get absorbed and I read the remaining passing light. I will try a lens if the amplifier doesn't cut it. Thanks!

The light comes from a fiber optic cable with a 1mm diameter, so I can't put them in parallel. I though about using lenses but I prefer an electronics-based solution than a mechanical one, as I would need to worry about the focal length and the lens diameter.

A transimpedance amplifier is a great idea, maybe I will add it as a preamplifier then amplify the signal to the desired output using another amplifier so I can get rid of the MOhm resistors. The feedback capacitor looks promising. I will build another iteration with all the comments in mind and will post the updates. Thanks

I tried the circuit with two amplifiers with feedback resistors of 50k value and the noise was reduced drastically. I used PCBs in both circuits and will add the decoupling capacitors in the next iteration. I am thinking to add a transimpedance amplifier instead of a pulldown resistor to convert the current output of the phototransistor to voltage.