Lemon contains tremendous shakti (energy). It has the capacity to grant that trait which is beyond the trigunas (the three attributes of Nature). Mother Goddess, in many instances, is seen wearing a garland of skulls. These are the skulls of the demons killed by her. This reflects Her compassion, mercy and immeasurable love towards those demons killed. Strewing together a garland of lemons and placing around the deity’s neck symbolizes the garland of skulls that she wears.
Coconut symbolizes the head. In those situations where coconuts are not available, lemons are offered to the deity. If 2 lemons were offered to the Guru, he would normally return 1 lemon as his blessing. The juice of the lemons offered to the Lord is generally consumed as prasadam. As per medical science, lemon juice taken in with a pinch of salt, sugar and honey is considered as a great remedy for many illnesses.
-Glimpses of Bhaktimala 4