I'll analyze the performance of different Affinity variants across all formats to find which has the highest win percentage.
Based on my analysis of Affinity variants across all formats over the past 60 days, Grixis Affinity in Pauper has the highest win percentage at 54.5%. This variant recorded 193 wins against 161 losses across 80 tournament entries, significantly outperforming other Affinity builds.
The traditional Modern Affinity deck sits at 47.3% winrate with 132 entries, while Esper Affinity in Pauper underperforms at just 37.5% with only 13 entries. The Grixis variant's superior performance suggests it's better positioned in the current Pauper metagame, likely benefiting from access to powerful removal and card selection that the red and black colors provide.
Sources
Data from 43 Pauper tournaments: 51.2% MTGO, 48.8% Melee. Recent tournaments include:
https://www.mtgo.com/decklist/pauper-challenge-32-2025-09-1412814292
https://melee.gg/Decklist/View/ff9be328-20e4-419c-95e8-b35700303374
https://melee.gg/Decklist/View/a9785ba5-4f68-4f49-9a87-b35401320b46