The new system will allow manufacturers and consumers to know the exact origin and production conditions of cocoa beans, the main ingredient in chocolate.
It will also introduce a new payment system aimed at ensuring farmers get a fair wage.
The move comes in response to plans by the European Union to ban imports of commodities and products linked to deforestation and human rights abuses.
"The objectives of our traceability system is to control the origins and the entire circuit of beans, fight against deforestation and pay the guaranteed price to farmers," said Yves Brahima Kone, head of the Cocoa and Coffee Council (CCC).
Currently, exporters have their own traceability systems that are not compatible with one another and do not make it possible to accurately determine the route of Ivorian beans from production to market.
The world's top cocoa producer, which accounts for around 40% of global output, has been criticised over the years for using thousands of child labourers in farms, and destroying large areas of forests and national parks to expand production.
Kone said the CCC had been developing software to trace cocoa beans from farms to storage centres and then to ports, but the missing link had been from farms to storage centres.
"Now that we have a reliable database on all farmers, the geographic location, dimensions and GPS coordinates of their farms, we can trace the origin of beans from the plantations to close the loop," Kone said.
He added the new system, backed by partners including chocolate makers, environmental groups and non-governmental organisations, would enable farmers to get the guaranteed farmgate price following the integration of an electronic payment system in partnership with Visa.