Cocoa pod husk (CPH) is a main by-product in cocoa processing industry and rich in alkaloids, which display some potent pharmacological properties such as stimulatory effects on the central nervous, gastrointestinal, cardiovascular, renal, and respiratory systems. This study aimed to utilize the CPH and various encapsulating materials (maltodextrin, gum Arabic, and chitosan) for production of microencapsulated powder rich in alkaloids. Physicochemical properties in terms of moisture content (MC), water activity (aw), water soluble index (WSI), density and morphology, bioactive compounds including total alkaloids content (TAC), total phenolics content (TPC), total flavonoids content (TFC) and total saponins content (TSC), as well as antioxidant activity comprising ABTS/DPPH radical scavenging capacity (ARSC/DRSC) and ferric/cupric reducing antioxidant capacity (FRAP/CUPRAC) of powder rich in alkaloids from the CPH extract with and without microencapsulation were then analyzed and compared. The results showed that the MC and aw of microencapsulated powders (4.78 to 5.88% and 0.46 to 0.51, respectively) were lower than those of powder without microencapsulation (9.64% and 0.54, respectively). Use of maltodextrin and gum Arabic (9:1 w/w) as the wall materials for microencapsulation of the CPH extract obtained the greatest levels of TPC, TFC, TSC, DRSC, FRAP and CUPRAC (14.91 mg GAE, 22.69 mg CE, 113.21 mg EE, 24.59, 2.92 and 92.68 mg TE per g dried sample, respectively), while use of 100% maltodextrin resulted in the maximum amounts of TAC and ARSC (646.96 mg AE/g dried sample and 36.27 mg TE/g dried sample, respectively). Based on the obtained results, the mixture of maltodextrin and gum Arabic (9:1 w/w) was recommended to microencapsulate the alkaloids-enriched CPH extract for potential application in the nutraceutical and functional food industries.