In 1302 his wardship and marriage were granted to John de Warenne, earl of Surrey (d. 1304), whose granddaughter Alice (the daughter of William (V) de Warenne) he married in 1305, after initially refusing her. He was granted seisin of his inheritance in April 1306, and knighted by Edward I on 22nd May, along with the prince of Wales, the future Edward II.

Following Edward I's death Fitzalan witnessed Piers Gaveston's creation as earl of Cornwall on 6th August 1307, and at the new king's coronation on 25th February 1308 he acted as butler and bearer of the royal robes. He soon joined the opposition to Gaveston, however, failing to attend the Stamford parliament of 1309, and in the parliament of March 1310 he was chosen to be one of the twenty-one lords ordainer commissioned to reform the realm. When Gaveston returned from exile in January 1312, Fitzalan joined the league which swore to hunt him down, and in June he was one of the four earls present at Gaveston's trial in Warwick Castle, following which the favourite was summarily executed on nearby Blacklow Hill. Although formally pardoned by the king in 1313, Fitzalan remained disaffected; he refused to accompany the royal campaign to Scotland which ended in disaster at Bannockburn in June 1314, and was prevented by Edward II from acquiring the lordship of Caus from Sir Peter Corbet in 1315. He was also appointed to the commission of reform set up by the earl of Lancaster in February 1316. During the next year or two, however, perhaps disillusioned with Lancaster, he gradually returned to the king's side: on 19th November 1316 he was appointed warden of the Scottish march, apparently against Lancaster's wishes, and he helped to negotiate the treaty of Leake of August 1318, which temporarily healed the breach between Lancaster and the king, and in which he was nominated as one of the council to be about the king's person.

Fitzalan was with the king at the siege of Berwick in September 1319, and when the ‘Despenser war’ broke out in the following year, he declined to join the marcher coalition, so that in 1321 his castle at Clun was attacked by the Mortimers. By this time his adherence to the king's party had been sealed by the marriage, on 9th February 1321, at the king's manor of Havering atte Bower, of his eldest son, Richard, to Isabella, daughter of the younger Hugh Despenser. Although he agreed—out of fear, so he said—to the exile of the Despensers in August 1321, three months later, having taken part in the siege of Leeds Castle in October, he advised the clergy on the king's behalf to revoke the sentence. In the winter of 1321–2 he joined the royal campaign to crush the marcher rebellion. He was appointed justice of Wales on 5th January 1322, and persuaded the Mortimers to surrender in the same month; he agreed to the proclamation of Lancaster and his adherents as traitors on 11th March, and he was one of the judges who condemned Lancaster to death at Pontefract Castle on 22nd March. Fitzalan was well rewarded for his loyalty with the forfeited estates of rebels, including the Mowbray lordships in the Isle of Axholme and the Mortimer lordship of Chirk, which bordered his patrimonial lordship of Oswestry. He took part in the Scottish campaign of 1322, remained justice of Wales until 1326, and had his reversionary right in the inheritance of John de Warenne, earl of Surrey, confirmed in the same year.

When the revolution of 1326 came, therefore, it was inevitable that Fitzalan would be one of Isabella and Mortimer's prime targets. He fled west with the king but was captured at Shrewsbury by John Charlton of Powys, taken to Queen Isabella at Hereford, and charged with being an accomplice of the Despensers, consenting to Lancaster's death, and plotting against the queen. He was beheaded—at Mortimer's insistence, so it was said—at Hereford on 17th November, by the hand of a worthless wretch (vilissimi ribaldi) who, according to the Llandaff chronicle, took twenty-two strokes to sever his head (BL, Cotton MS Nero A. iv, fol. 57v). His body was later removed to Haughmond Abbey, the traditional burial place of the Fitzalans. His considerable store of treasure was looted from Chichester Cathedral and the priory of the Holy Trinity in London, and much of it eventually found its way into Isabella's and Mortimer's coffers; he was convicted of treason and his heir disinherited. His castle and honour of Arundel, said to be worth £600 per annum, was given to the earl of Kent, and all his lands in Shropshire and north Wales to Roger Mortimer.

Although Fitzalan is frequently criticized by historians for his changes of allegiance, these were far from untypical of the peerage during Edward II's troubled reign, and the accusations levelled against him after his death concerning his complicity in the ‘Despenser regime’ were the inevitable consequence of its circumstances. He provides, in fact, a rare example of Edward II's ability to win to his side, and retain the allegiance of, a magnate who had earlier opposed him.

Edmund and Alice had  six children:

Richard FitzAlan, 10th Earl of Arundel who succeeded to the earldom following Mortimer's downfall in 1330

Edmund FitzAlan who entered the church

Michael FitzAlan  who entered the church;

Alice FitzAlan who married John de Bohun heir to the earldom of Hereford, in 1325

Aleyne FitzAlan who married Roger Lestrange of Knockin in c.1338

Jane FitzAlan who is said to have married Lord Lisle