An In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</sub> As/indium phosphide (InP) avalanche photodiode (APD) with a separate absorption, grading, charge, and multiplication (SAGCM) structure is epitaxially grown by molecular beam epitaxy (MBE). The resulting material is studied using X-ray diffraction (XRD), photoluminescence (PL), and scanning transmission electron microscopy. The activation energy extracted from the dark current of the APD indicates that it is dominated by the generation–recombination (G–R) process. Deep low-temperature PL peaks reveal the existence of an <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${E}_{v} + 0.42$ </tex-math></inline-formula> -eV deep energy level defect in the indium–gallium–arsenide (InGaAs) absorber layer, which is considered to be a result of point defects caused by Ga-poor or In-poor MBE growth conditions. The effect of the defect on the dark current is confirmed using numerical calculation methods.