But Samoothiri faced defeat in the next attack on Perumpadappu. The Perumpadappu Rajas appealed to their friend Vellaattiri for help and Vellaattiri send his armies across. Their combined army attacked Samoothiri's forces and a bloody war ensued for three days, at the end of which Samoothiri's army was on the retreat.
 

After a period of uneasy calm Samoothiri sent his armies westward from Ponnani and invaded Nedunganad. This small kingdom was annexed by Samoothiri soon afterwards - Nedungattiri, the Raja of this place, was given certain rights of supervision over the temple of Cherplassery, and a subsistence allowance.
 

1405 A.D. - Samoothiri continued his aggression on Perumpadappu Rajas. The Perumpadappu Rajas, or Rajas of Kochi as they came to be known later, were forced to shift their capital from Thiruvanchikkulam to Kochi.
 

Pantalur and Kottakkal came under Samoothiri only after a protracted struggle. These areas were under Karuvayoor Moosad, the Brahmin chief minister of Vellaattiri. Neither machinations of Mangattachan nor threat of war made his submission possible. Instead he even indulged in provocative treachery by inviting Thinayencheri Ilayathu, a minister of Samoothiri, to his home to negotiate a marriage proposal, and killing him. A furious Samoothiri decided to avenge the death of his minister and sent a huge army under Munalpad (third prince). After a bloody war which lasted for about 12 years, in which all types of treachery imaginable was performed by both sides, Samoothiri's army trapped the Moosad at Padapparamba, captured him and put him to death. The loss of this brave and fiercely loyal chief minister was the greatest blow to Vellaattiri after the Thirunavaya war. These captured areas were given to Varakkal Paranambi, a minister of Samoothiri.
 

Unable to withstand Samoothiri's attacks, Kochi Raja finally accepted Samoothiri's rule and became his feudatory.