She worked at a number of sites, but is best known for her excavations at Mucking, a major Anglo-Saxon settlement and associated cemetery, with finds ranging from the Stone Age to the Medieval period.

Jones' work at Mucking, as well as her role in founding the campaign group Rescue, was influential in the establishment of modern commercial archaeology in Britain.

The site had been discovered in aerial photographs taken by Kenneth St Joseph and confirmed in a small fieldwalking survey by the Thurrock Local History Society.

[6][7] Jones quickly concluded that the crop marks at Mucking represented an extensive site with Iron Age, Roman, Anglo-Saxon and early Medieval remains.

[3] The site was run on a tight budget, and the living conditions there were notorious:[1] The conditions were tough: accommodation ranged from your own tent to leaking huts; food was the cheapest line from the cash and carry, creatively supplemented with wild gleanings (I once asked the cook what was for supper, to learn she had spent her afternoon removing, as instructed, mouse-droppings from a sack of rice); and entertainment consisted of a night-time drive round one of the uncannily-automated oil-refining stations along the coast.Jones herself also gained a reputation as an eccentric[1] and intimidating[10] figure: "indomitable, formidable, disinclined to suffer fools but very kind to those she considered worth helping, dedicated and inventive".

Margaret became the patron of the Thurrock Local History Society (the source of many volunteers to the Mucking excavation) and sat on many other archaeology committees in Essex.

Jones and her colleagues were paid only a day-rate for time spent digging and the costs directly incurred, precluding any post-excavation analysis or publication of their finds.

[1] This initiative was ultimately successful, increasingly shifting the labour of pre-development excavation from volunteers to professional archaeologists, and culminating in the creation of modern commercial archaeology with the publication of Planning Policy Guidance Note 16 in 1991.

[11] According to her obituarist Mike Pitts, Jones also influenced the formation of modern rescue archaeology in Britain by demonstrating "dogged salvage excavation on a grand scale" at Mucking.

[3] Ultimately, the final publication of Mucking was undertaken by others (English Heritage and the Cambridge Archaeological Unit),[1][3] the first volume of which did not appear until 2015, fourteen years after Jones' death.