Economic prosperity returned, marked by the cattle market on the Gravier authorised in 1610 and the market for prunes and small livestock at the Porte du Pin. Many private and public buildings were constructed. The River Garonne was the main artery of this prosperity. 

The first half of the 17th century also saw a religious revival and Agen bristled with bell towers. 
However, the town still needed the protection of its ramparts against hostile troops and disease, as the region continued to be a theatre of war, in particular in the time of the Fronde. 
The 17th century also experienced severe climate changes with droughts, floods, plague and famine.
As a result, Agen gradually lost its wealth and towards the middle of the century was unable to meet its debts. Appeals to the central government and subsequent attempts by Richelieu to raise taxes led to riots in 1635.

After the plague and famine of 1651, Agen was able to regain some of its prosperity. The introduction of maize as a crop helped the rural economy, but the countryside was to continue its steady decline, while the Revocation of the Edict of Nantes and the flight of the Protestants deprived the Agen region of some of its more dynamic elements.