NOVELTY - Jatropha Methyl Ester and by-products from encapsulated seeds of Jatropha are prepared by mechanically deshelling capsulated seeds of Jatropha; expelling Jatropha oil, Jatropha oil cake having 4-6% nitrogen and waste oil sludge from Jatropha seeds; neutralizing Jatropha oil with base; and transesterifying one part of neutralized Jatropha oil with alcohol and base and separating crude glycerol layer and crude Jatropha methyl ester.    USE - Method for integrated preparation of Jatropha Methyl Ester and by-products (claimed), useful in production of biodiesel.    ADVANTAGE - The method is capable of producing biodiesel with least energy input and zero effluent discharge. It eliminates the need for distillation of methanol for its recovery. The sun dried whole seed capsules enhance the keeping characteristics and the oil has a free fatty acid content of only 0:5-2 % when the seeds are encapsulated thus increasing the yield of methyl ester.    DETAILED DESCRIPTION - Integrated preparation of Jatropha Methyl Ester (JME) and by-products from encapsulated seeds of Jatropha containing 1.06% of free fatty acids (FFA), comprises (A) mechanically deshelling capsulated seeds of Jatropha in deshelling machine to obtain Jatropha shells and Jatropha seeds; (B) expelling Jatropha oil, Jatropha oil cake having 4-6% nitrogen and waste oil sludge from Jatropha seeds using oil expeller; (C) neutralizing Jatropha oil with base; (D) transesterifying one part of neutralized Jatropha oil with alcohol and base with stirring for 10-20 minutes and separating crude glycerol layer (GL1) and crude Jatropha methyl ester (JME); (E) washing crude JME 3 times with pure glycerol layer to separate 3 impure glycerol layers (GL2, GL3 and GL4) containing methanol and potassium hydroxide (KOH) to obtain Glycerol washed JME-G3W; (F) purifying JME-G3W to remove alkali metal impurities; (G) treating part of remaining neutralized oil with glycerol layers (GL5) and obtaining JME and glycerol layer (GL6); (G) separating JME and glycerol layer (GL6); (H) treating glycerol layer (GL6) with remaining part of neutralized oil for mopping up of methanol to obtain JME and glycerol layer (GL7); (I) separating JME and glycerol layer (GL7); (J) using glycerol layer (GL7) directly for production of polyhydroxyalkanoates (PHAs) or for neutralization of alkali with sulfuric acid to obtain pure glycerol and still bottom (GL8); (K) combining JME-G3W and JME to obtain combined methyl ester; and (L) transesterifying combined methyl ester with methanolic KOH to yield pure Jatropha methyl ester (Biodiesel) having total glycerol of 0.088% and free glycerol of 0.005%.