- Internal Conflicts: The Songhai Empire faced numerous internal power struggles and conflicts, often marked by political instability, rivalries among influential families and succession crises.
- Drought and Famine: The region experiences sever drought that led to widespread crop failures and famine. These climatic conditions weakened the empire's agricultural production and destabilized the economy.
- Lack of Trade: Trans-Saharan trade, a crucial source of wealth and resources for the Songhai Empire, also faced challenges due to changes in trade routes, competition from other trading powers and disruptions in the gold trade.
- Military Defeats: The Songhai Empire suffered a significant military defeat in the Battle of Tondibi (1591) against the invading Moroccan forces led by Sultan Ahmad al-Mansur. The Moroccans used advanced firearms, defeating the empire's less advanced army and occupying key regions.
- Administrative Weaknesses: The empire faced administrative challenges, such as the vastness of its territories, the control over distant provinces, and the effectiveness of its government structures.
- Political Fragmentation: Following the defeat at Tondibi, the empire broke into smaller states and faced internal division and fragmentation, making it harder to maintain the empire's unity.