Ca as an unintentional impurity has been investigated in III-nitride layers grown by molecular beam epitaxy (MBE). It is found that Ca originates from the substrate surface, even if careful cleaning and rinsing procedures are applied. The initial Ca surface coverage is ∼1012 cm−2, which is consistent with previous reports on GaAs and silicon wafers. At the onset of growth, the Ca species segregates at the growth front while incorporating at low levels. The incorporation rate is strongly temperature dependent. It is about 0.03% at 820 °C and increases by two orders of magnitude when the temperature is reduced to 600 °C, which is the typical growth temperature for InGaN alloy. Consequently, [Ca] is as high as 1018 cm−3 in InGaN/GaN quantum well structures. Such a huge concentration might be detrimental for the efficiency of light emitting diodes (LEDs) if one considers that Ca is potentially a source of Shockley-Read-Hall (SRH) defects. We thus developed a specific growth strategy to reduce [Ca] in the MBE grown LEDs, which consisted of burying Ca in a low temperature InGaN/GaN superlattice (SL) before the growth of the active region. Finally, two LED samples with and without an SL were fabricated. An increase in the output power by one order of magnitude was achieved when Ca was reduced in the LED active region, providing evidence for the role of Ca in the SRH recombination.