Prick your conscience
Definition 1 of 1
Pro Tip 1/3Metaphorical Sting
The phrase suggests a sharp mental discomfort as if conscience has been physically stung. 
Cheating in the exam pricked his conscience for weeks.
Pro Tip 2/3Emotional Trigger
It is used when an action or event triggers a feeling of guilt or remorse. 
Lying to her parents really pricked her conscience.
Pro Tip 3/3Reflective Moments
Often used to describe a moment of reflection that causes a change of heart or behavior. 
Ignoring the charity appeal pricked his conscience later on.