The Roman period also saw an intensification of irrigation development, most notably through the use of underground qanats. These certainly enabled heightened agricultural production in the Mediterranean and pre-desert regions of North Africa. Farming of the land was also encouraged by the state, either through direct taxation or through the management of imperial estates (of which there were many), so there was impetus to develop above and beyond subsistence and transhumance in order to satisfy these demands. Grain is only one example, Tunisia, Algeria, and Libya (both Tripolitania and Cyrenaica) also grew grapes and olives and produced large amounts of wine and olive oil.

The end of the Roman period in the fifth century (and then again after the Byzantine reconquest in the 6th) meant a lessened demand for the agricultural products across North Africa as it ceased export to Rome and its other provinces. Without the high demand for their products, North African farmers could no longer safely invest in developed agricultural production (including irrigation systems, but also multi-press facilities for olive oil or wine production) without fearing for major losses in their returns. We must also consider the effects of increased political instability in the wake of the Vandalic conquest and the activity of a number of nomadic tribes which could no longer be monitored by the Roman army.

An example can be found in the hinterland of the town of Diana Veteranorum in modern Algeria, where the removal of the Roman military and subsequent detachment from the Mediterranean market system led to a disintegration of the local agricultural economy that had been largely based on the production of textiles. The region is basically abandoned in the 6th century.

See E. Fentress 2013 "Diana Veteranorum and the dynamics of an inland economy," in L. Lavan (ed.) Local Economies? Production and Exchange of Inland Regions in Late Antiquity. pp. 315-42 for the details of this study.

The region underwent desertification . Or rather continued he process of desertification that had been going on for several thousand years.

During the roman period you could use horses in overland trade . A few centuries later the Sahara entered the last stages of desertification and is the bone dry wast land we know it . I'm at work so ill link sources when I get home

/u/at_dawn_they_come actually covers most of it. But adding an even simpler point, after the Arab conquest of the Levant (and some would argue even before then with the Vandal conquest of Roman Africa), the Mediterranean was no longer under complete Roman control, and was a contested space which became brimming with pirates and raiders, making it unsafe for large scale trade.

Which meant the bulk grain and trade shipping that used to occur from Africa to Rome ceased. Combined with the existing tendencies toward regionalization after the fragmentation of the empire and with the caliphate's grain supplied by egypt, and you have the collapse/withering away of the demand for intensive agriculture for export in Africa, as well as its ancillary pottery and export good industries (which relied on the bulk grain trade for piggyback shipping).

Something to think about. From the Arab conquest in the 7th century, it wasn't until the 20th century (maybe late 19th) that such bulk cross mediterranean trade existed again due to security concerns. That is a long time for Algeria/Tunisia to be without an export market for their goods, when in antiquity it was just a short hop right across the sea. Which is why those industries didn't last past the collapse of the empire.