Precision agriculture requires new technologies for rapid diagnosis of plant stresses, such as nutrient deficiency and drought, before the onset of visible symptoms and subsequent yield loss. Here, we demonstrate a portable Raman probe that clips around a leaf for rapid, in vivo spectral analysis of plant metabolites including carotenoids and nitrates. We use the leaf-clip Raman sensor for early diagnosis of nitrogen deficiency of the model plant Arabidopsis thaliana as well as two important vegetable crops, Pak Choi (Brassica rapa chinensis) and Choy Sum (Brassica rapa var. parachinensis). In vivo measurements using the portable leaf-clip Raman sensor under full-light growth conditions were consistent with those obtained with a benchtop Raman spectrometer measurements on leaf-sections under laboratory conditions. The portable leaf-clip Raman sensor offers farmers and plant scientists a new precision agriculture tool for early diagnosis and real-time monitoring of plant stresses in field conditions.