The Khasi mandarin (Citrus reticulata Blanco) fruit is an important commercially grown citrus cultivar of Meghalaya and it suffers from quality deterioration due to post harvest diseases. The present study was undertaken to estimate the losses due to diseases, identification of pathogen associated with disease, evaluate the efficacy of different plants extract to control the diseases and their effect on the quality during storage. Water extracts of different plant leaves viz., Margosa (Azadirachta indica), Holy basil (Ocimum sanctum) and Aloe Vera (Aloe barbedensis) and their combinations were used. Treated fruits were stored under open condition at room temperature (RT) i.e. 14.5-18.4�C and relative humidity i.e. 70�2% and in corrugated fiber board (CFB) boxes for evaluating the quality of fruits during storage. The survey revealed that post harvest diseases caused 17.75-19.28% losses and the major pathogens involved were Penicillium spp. Penicillium brevicompactum was regularly isolated from infected fruits and was used in subsequent investigations. Fruits dipped in Holy basil solution (50%) showed minimum percent disease index (POI) of 2.67% and 1.33% followed by Margosa with PDI of 3.33% and 2.67% in open at RT and CFB boxes respectively. Holy basil extract significantly inhibited spores germination and mycelial growth to an extent of 96.52% and 95.69% respectively followed by Margosa leaf extract at 25�C. The study on physiological changes due to treatments revealed that Holy basil treated fruits packed in CFB boxes recorded the minimum physiological loss in weight (20.01%) followed by Margosa (20.57%) for a maximum storage of 28 days. Decay losses also showed a similar trend of minimum total loss (20%). The losses in peel weight, pulp weight and juice content of fruits were also minimum i.e. 20.80%, 67.98% and 39.26% respectively in Holy basil treated fruits at the end of storage period. The maximum increase in TSS (13.46%) and total sugar (8.39%) was recorded in fruits treated with Holy basil. Minimum decrease in acidity (0.69%) and ascorbic acid (29.69 mg/100ml.) was also recorded in fruits treated with Holy basil. The sensory analysis of Khasi mandarin during storage revealed that fruits treated with Holy basil and packed in CFB boxes recorded maximum sensory scores in terms of taste (7.33), texture (7.27), appearance (7.47), flavour (7.60), colour (7.60) and overall acceptability (7.33) as compared with other treatments. Key words: Khasi mandarin, Penicillium brevicompactum, Margosa, Holy basil, Aloe Vera, Corrugated fiber board box