Conditional and joint (COJO) analysis is a standard post GWAS analysis to quantify the number of independent SNP associations. GWAS meta-analyses are increasingly conducted across multiple ancestry groups and the validity of applying the standard single ancestry COJO algorithm to the multi-ancestry context is unclear. We have developed a multi-ancestry version of COJO Simulations and real-data analyses show that Manc-COJO improves the detection of independent association signals and reduces false positives compared to COJO and ad hoc adaptations for multi-ancestry use. This work extends general understanding of multi-ancestry GWAS and transferability of polygenic risk scores across ancestries.